Duplex dual-labeled fluorescence probe-based melting curve and endpoint genotyping assays for genotyping of rs2000999 and haptoglobin gene deletion

Haptoglobin (Hp) is a hemoglobin-binding serum glycoprotein. Some variations in the Hp gene (HP) or Hp-related gene (HPR), including a single-nucleotide polymorphism in intron 2 of HRP, rs2000999, and a complete deletion of the HP gene (HP^del), one of the rare variants of HP, have been reported to correlate with the serum cholesterol concentration as well as the serum Hp concentration. In this study, we developed a duplex dual-labeled fluorescence probe-based method to simultaneously determine the rs2000999 G > A polymorphism by melting curve genotyping and the zygosity of HP^del by endpoint genotyping. This method was then validated by using the genomic DNA from 94 Japanese subjects for whom genotypes of rs2000999 and HP^del zygosity had already been determined. The results obtained with this method were in perfect agreement with the previous ones. Thus, the present method enables us to estimate these two polymorphisms in relatively large-scale groups of subjects, especially in Asian populations where the HP^del is distributed.     

2020年诺贝尔化学奖的再思考——归属争议与原创表彰

2020年诺贝尔化学奖授予两位女性科学家——埃马纽埃尔.卡彭蒂耶和詹妮弗.杜德纳。回顾CRISPR-Cas9技术的发展史,她们完整地说明了该技术的原理、作用,并研发了CRISPR-Cas9基因编辑技术,符合诺贝尔奖奖励原创的要求,是争议最小的获奖者人选。专利和诺贝尔奖在维护发明者权益、促进科学的发展上都具有重要的作用,且不能仅以其中一项的结果判断另一项的归属,目前的归属差异不影响非商业应用的学术研究,并客观上推动了原创研究的产出。进一步思考原创的概念,明确基础科学的定位,加强对创新人才的鼓励和支持,注重诺贝尔奖颁奖历史的梳理,也是本次诺贝尔奖给予我们的启示。     

DCE-MRI参数联合IFIT1基因对腰椎间盘突出患者椎间盘退变程度的评估价值

探讨DCE-MRI参数及IFIT1基因对腰椎间盘突出症(LDH)患者椎间盘退变(IDD)程度的评估价值。随机选取确诊的66例LDH患者作为研究对象,根据改良Pfirrmann分级法将患者分为2组:轻中度IDD(Ⅰ~Ⅲ级)组(46例)和重度IDD(Ⅳ~Ⅴ级)组20例。通过DCE-MRI检查考察患者的K-trans值,采用日本骨科学会评分(JOA)评估腰椎功能,采用视觉模拟评分法(VAS)评估腰部疼痛,采用RT-PCR检测外周血单个核细胞(PBMC)中IFIT1的mRNA表达。轻中度IDD组的K-trans值显著低于重度IDD组。轻中度IDD组患者PBMC中的IFIT1 mRNA相对表达量显著低于重度IDD组。K-trans值与PBMC中的IFIT1 mRNA水平和VAS评分正相关,与JOA评分负相关(P<0.05)。PBMC中的IFIT1 mRNA水平与VAS评分正相关,与JOA评分负相关(P<0.05)。K-trans值和PBMC中的IFIT1 mRNA水平联合诊断重度IDD的AUC值、敏感性和特异性分别为0.991、91.3%和100.0%,AUC值和特异性均高于单独诊断。DCE-MRI检查中的K-trans值联合PBMC中的IFIT1 mRNA水平可用于LDH患者IDD程度的诊断。     

In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria

The impact of lifestyle on shaping the genome content of an organism is a well-known phenomenon and cytochrome P450 enzymes (CYPs/P450s), heme-thiolate proteins that are ubiquitously present in organisms, are no exception. Recent studies focusing on a few bacterial species such as Streptomyces, Mycobacterium, Cyanobacteria and Firmicutes revealed that the impact of lifestyle affected the P450 repertoire in these species. However, this phenomenon needs to be understood in other bacterial species. We therefore performed genome data mining, annotation, phylogenetic analysis of P450s and their role in secondary metabolism in the bacterial class Gammaproteobacteria. Genome-wide data mining for P450s in 1261 Gammaproteobacterial species belonging to 161 genera revealed that only 169 species belonging to 41 genera have P450s. A total of 277 P450s found in 169 species grouped into 84 P450 families and 105 P450 subfamilies, where 38 new P450 families were found. Only 18% of P450s were found to be involved in secondary metabolism in Gammaproteobacterial species, as observed in Firmicutes as well. The pathogenic or commensal lifestyle of Gammaproteobacterial species influences them to such an extent that they have the lowest number of P450s compared to other bacterial species, indicating the impact of lifestyle on shaping the P450 repertoire. This study is the first report on comprehensive analysis of P450s in Gammaproteobacteria.     

Tiling solutions for optimal biological sensing

Biological systems, from cells to organisms, must respond to the ever-changing environment in order to survive and function. This is not a simple task given the often random nature of the signals they receive, as well as the intrinsically stochastic, many-body and often self-organized nature of the processes that control their sensing and response and limited resources. Despite a wide range of scales and functions that can be observed in the living world, some common principles that govern the behavior of biological systems emerge. Here I review two examples of very different biological problems: information transmission in gene regulatory networks and diversity of adaptive immune receptor repertoires that protect us from pathogens. I discuss the trade-offs that physical laws impose on these systems and show that the optimal designs of both immune repertoires and gene regulatory networks display similar discrete tiling structures. These solutions rely on locally non-overlapping placements of the responding elements (genes and receptors) that, overall, cover space nearly uniformly.     

Transplantation of betacellulin-transduced islets improves glucose intolerance in diabetic mice

Type 1 diabetes is an autoimmune disease caused by permanent destruction of insulin-producing pancreatic β cells and requires lifelong exogenous insulin therapy. Recently, islet transplantation has been developed, and although there have been significant advances, this approach is not widely used clinically due to the poor survival rate of the engrafted islets. We hypothesized that improving survival of engrafted islets through ex vivo genetic engineering could be a novel strategy for successful islet transplantation. We transduced islets with adenoviruses expressing betacellulin, an epidermal growth factor receptor ligand, which promotes β-cell growth and differentiation, and transplanted these islets under the renal capsule of streptozotocin-induced diabetic mice. Transplantation with betacellulin-transduced islets resulted in prolonged normoglycemia and improved glucose tolerance compared with those of control virus-transduced islets. In addition, increased microvascular density was evident in the implanted islets, concomitant with increased endothelial von Willebrand factor immunoreactivity. Finally, cultured islets transduced with betacellulin displayed increased proliferation, reduced apoptosis and enhanced glucose-stimulated insulin secretion in the presence of cytokines. These experiments suggest that transplantation with betacellulin-transduced islets extends islet survival and preserves functional islet mass, leading to a therapeutic benefit in type 1 diabetes.     

Non‐Heme Dioxygenase Catalyzes Atypical Oxidations of 6,7‐Bicyclic Systems To Form the 6,6‐Quinolone Core of Viridicatin‐Type Fungal Alkaloids

The 6,6‐quinolone scaffold of the viridicatin‐type of fungal alkaloids are found in various quinolone alkaloids which often exhibit useful biological activities. Thus, it is of interest to identify viridicatin‐forming enzymes and understand how such alkaloids are biosynthesized. Here an Aspergillal gene cluster responsible for the biosynthesis of 4′‐methoxyviridicatin was identified. Detailed in vitro studies led to the discovery of the dioxygenase AsqJ which performs two distinct oxidations: first desaturation to form a double bond and then monooxygenation of the double bond to install an epoxide. Interestingly, the epoxidation promotes non‐enzymatic rearrangement of the 6,7‐bicyclic core of 4′‐methoxycyclopenin into the 6,6‐quinolone viridicatin scaffold to yield 4′‐methoxyviridicatin. The finding provides new insight into the biosynthesis of the viridicatin scaffold and suggests dioxygenase as a potential tool for 6,6‐quinolone synthesis by epoxidation of benzodiazepinediones.     

Tetramethylguanidinium‐polyallylamine (Tmg‐PA): A new class of nonviral vector for efficient gene transfection

Highly toxic polyallylamine (PA) was reacted with a varying amount of a novel linker, 6‐(N,N,N′,N′‐tetramethylguanidinium chloride) hexanoic acid (Tmg‐HA), to prepare a series of tetramethylguanidinium‐PA (Tmg‐PA) polymers, which were used as vectors for gene transfection. The extent of attachment of the linker, Tmg‐HA, to the PA backbone was determined by 2,4,6‐trinitrobenzene sulfonic acid assay. The modified polymers (Tmg‐PAs), when complexed with pDNA, exhibited good condensation ability. The nanoparticles, so formed, were characterized by their size and zeta potential and were subsequently evaluated for their toxicity and transfection ability on various mammalian cells, viz., HeLa, CHO, and HEK 293 cells. Mobility shift assay revealed that on increasing the percent substitution of Tmg‐HA onto PA (from Tmg‐PA1 to Tmg‐PA6), relatively higher amounts of modified polymers were required to retard the mobility of a fixed amount of DNA. Besides, Tmg‐PA polymers provided sufficient protection (ca. 84–88%) to bound DNA against nucleases and one of the formulations, Tmg‐PA2 (ca. 15% substitution) displayed the highest transfection efficiency outcompeting the commercial transfection reagent, Lipofectamine? with minimal cytotoxicity. More impressively, the transfection efficiency increased despite recording a decrease in the buffering capacity of the grafted polymers suggesting that buffering capacity is not the sole parameter in determining the gene delivery efficiency of a vector system. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Cloning, expression, and characterization of thermostable region of amylopullulanase gene from Thermoanaerobacter ethanolicus 39E

The bifunctional activities of α-amylase and pullulanase are found in the cloned recombinant amylopullulanase. It was encoded in a 2.9-kb DNA fragment that was amplified using polymerase chain reaction from the chromosomal DNA of Thermoanaerobacter ethanolicus 39E. An estimated 109-kDa recombinant protein was obtained from the cloned gene under the prokaryotic expression system. The optimum pH of the recombinant amylopullulanase was 6.0. The most stable pH for the α-amylase and pullulanase activity was 5.5 and 5.0, respectively. The optimum temperature for the α-amylase activity was 90°C, while its most stable temperature was 80°C. Regarding pullulanase activity, the optimum temperature and its most stable temperature were found to be 80 and 75°C, respectively. Pullulan was found to be the best substrate for the enzyme. The enzyme was activated and stabilized by the presence of Ca²⁺, whereas EDTA, N-bromosuccinimide, and α-cyclodextrin inhibited its bifunctional activities. A malto-2–4-oligosac-charide was the major product obtained from the enzymatic reaction on soluble starch, amylose, amylopectin, and glycogen. A single maltotriose product was found in the pullulan hydrolysis reaction using this recombinant amylopullulanase. Kinetic analysis of the enzyme indicated that the K _m values of α-amylase and pullulanase were 1.38 and 3.79 mg/mL, respectively, while the V _max values were 39 and 98 μmol/(min · mg of protein), respectively.