How To Quantify a Genetic Firewall? A Polarity-Based Metric for Genetic Code Engineering

Genetic code engineering aims to produce organisms that translate genetic information in a different way from that prescribed by the standard genetic code. This endeavor could eventually lead to genetic isolation, where an organism that operates under a different genetic code will not be able to transfer functional genes with other living species, thereby standing behind a genetic firewall. It is not clear however, how distinct the code should be, or how to measure the distance. We have developed a metric (Δ_code) where we assigned polarity indices (clog D₇) to amino acids to calculate the distances between pairs of genetic codes. We then calculated the distance between a set of 204 genetic codes, including the 24 known distinct natural codes, 11 extreme-distance codes created computationally, nine theoretical special purpose codes from literature and 160 codes in which canonical amino acids were replaced by noncanonical chemical analogues. The metric can be used for building strategies towards creating semantically alienated organisms, and testing the strength of genetic firewalls. This metric provides the basis for a map of the genetic codes that could guide future efforts towards novel biochemical worlds, biosafety and deep barcoding applications.     

Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-Modular Coupling

The role of aminoacyl-tRNA synthetases (aaRS) in the emergence and evolution of genetic coding poses challenging questions concerning their provenance. We seek evidence about their ancestry from curated structure-based multiple sequence alignments of a structurally invariant “scaffold” shared by all 10 canonical Class I aaRS. Three uncorrelated phylogenetic metrics—mutation frequency, its uniformity, and row-by-row cladistic congruence—imply that the Class I scaffold is a mosaic assembled from successive genetic sources. Metrics for different modules vary in accordance with their presumed functionality. Sequences derived from the ATP– and amino acid– binding sites exhibit specific two-way coupling to those derived from Connecting Peptide 1, a third module whose metrics suggest later acquisition. The data help validate: (i) experimental fragmentations of the canonical Class I structure into three partitions that retain catalytic activities in proportion to their length; and (ii) evidence that the ancestral Class I aaRS gene also encoded a Class II ancestor in frame on the opposite strand. A 46-residue Class I “protozyme” roots the Class I tree prior to the adaptive radiation of the Rossmann dinucleotide binding fold that refined substrate discrimination. Such rooting implies near simultaneous emergence of genetic coding and the origin of the proteome, resolving a conundrum posed by previous inferences that Class I aaRS evolved after the genetic code had been implemented in an RNA world. Further, pinpointing discontinuous enhancements of aaRS fidelity establishes a timeline for the growth of coding from a binary amino acid alphabet.     

Characterization of Erysiphe necator-Responsive Genes in Chinese Wild Vitis quinquangularis

Powdery mildew (PM), caused by fungus Erysiphe necator, is one of the most devastating diseases of grapevine. To better understand grapevine-PM interaction and provide candidate resources for grapevine breeding, a suppression subtractive hybridization (SSH) cDNA library was constructed from E. necator-infected leaves of a resistant Chinese wild Vitis quinquangularis clone “Shang-24”. A total of 492 high quality expressed sequence tags (ESTs) were obtained and assembled into 266 unigenes. Gene ontology (GO) analysis indicated that 188 unigenes could be assigned with at least one GO term in the biological process category, and 176 in the molecular function category. Sequence analysis showed that a large number of these genes were homologous to those involved in defense responses. Genes involved in metabolism, photosynthesis, transport and signal transduction were also enriched in the library. Expression analysis of 13 selected genes by qRT-PCR revealed that most were induced more quickly and intensely in the resistant material “Shang-24” than in the sensitive V. pseudoreticulata clone “Hunan-1” by E. necator infection. The ESTs reported here provide new clues to understand the disease-resistance mechanism in Chinese wild grapevine species and may enable us to investigate E. necator-responsive genes involved in PM resistance in grapevine germplasm.     

Computational Functional Genomics-Based AmpliSeq™ Panel for Next-Generation Sequencing of Key Genes of Pain

The genetic background of pain is becoming increasingly well understood, which opens up possibilities for predicting the individual risk of persistent pain and the use of tailored therapies adapted to the variant pattern of the patient’s pain-relevant genes. The individual variant pattern of pain-relevant genes is accessible via next-generation sequencing, although the analysis of all “pain genes” would be expensive. Here, we report on the development of a cost-effective next generation sequencing-based pain-genotyping assay comprising the development of a customized AmpliSeq™ panel and bioinformatics approaches that condensate the genetic information of pain by identifying the most representative genes. The panel includes 29 key genes that have been shown to cover 70% of the biological functions exerted by a list of 540 so-called “pain genes” derived from transgenic mice experiments. These were supplemented by 43 additional genes that had been independently proposed as relevant for persistent pain. The functional genomics covered by the resulting 72 genes is particularly represented by mitogen-activated protein kinase of extracellular signal-regulated kinase and cytokine production and secretion. The present genotyping assay was established in 61 subjects of Caucasian ethnicity and investigates the functional role of the selected genes in the context of the known genetic architecture of pain without seeking functional associations for pain. The assay identified a total of 691 genetic variants, of which many have reports for a clinical relevance for pain or in another context. The assay is applicable for small to large-scale experimental setups at contemporary genotyping costs.     

Identification of Risk Genes Associated with Myocardial Infarction—Big Data Analysis and Literature Review

Acute myocardial infarction occurs when blood supply to a particular coronary artery is cut off, causing ischemia or hypoxia and subsequent heart muscle destruction in the vascularized area. With a mortality rate of 17% per year, myocardial infarction (MI) is still one of the top causes of death globally. Numerous studies have been done to identify the genetic risk factors for myocardial infarction, as a positive family history of heart disease is one of the most potent cardiovascular risk factors. The goal of this review is to compile all the information currently accessible in the literature on the genes associated with AMI. We performed a big data analysis of genes associated with acute myocardial infarction, using the following keywords: “myocardial infarction”, “genes”, “involvement”, “association”, and “risk”. The analysis was done using PubMed, Scopus, and Web of Science. Data from the title, abstract, and keywords were exported as text files and imported into an Excel spreadsheet. Its analysis was carried out using the VOSviewer v. 1.6.18 software. Our analysis found 28 genes which are mostly likely associated with an increased risk for AMI, including: PAI-1, CX37, IL18, and others. Also, a correlation was made between the results obtained in the big data analysis and the results of the review. The most important genes increasing the risk for AMI are lymphotoxin-a gene (LTA), LGALS2, LDLR, and APOA5. A deeper understanding of the underlying functional genomic circuits may present new opportunities for research in the future.     

Improved Bonding of Partially Osteomyelitic Bone to Titanium Pins Owing to Biomimetic Coating of Apatite

Increased fixation strength of the bone-pin interface is important for inhibiting pin loosening after external fixation. In a previous study, an apatite (Ap) layer was formed on anodically oxidized titanium (Ti) pins by immersing them in an infusion fluid-based supersaturated calcium phosphate solution at 37 °C for 48 h. In the present study, an Ap layer was also successfully formed using a one-step method at 25 °C for 48 h in an infusion fluid-based supersaturated calcium phosphate solution, which is clinically useful due to the immersion temperature. After percutaneous implantation in a proximal tibial metaphysis for four weeks in rabbits (n = 20), the Ti pin coated with the Ap layer showed significantly increased extraction torque compared with that of an uncoated Ti screw even with partial osteomyelitis present, owing to dense bone formation on the Ap layer in the cortical and medullary cavity regions. When the infection status was changed from “no osteomyelitis” to “partial osteomyelitis,” the extraction torque in the Ap group with “partial osteomyelitis” was almost identical to that for “no osteomyelitis” cases. These results suggest that the Ap layer formed by the room temperature process could effectively improve the fixation strength of the Ti pin for external fixation clinically even with partial osteomyelitis present.     

Discovery of Proteomic Code with mRNA Assisted Protein Folding

The 3x redundancy of the Genetic Code is usually explained as a necessity to increase the mutation-resistance of the genetic information. However recent bioinformatical observations indicate that the redundant Genetic Code contains more biological information than previously known and which is additional to the 64/20 definition of amino acids. It might define the physico-chemical and structural properties of amino acids, the codon boundaries, the amino acid co-locations (interactions) in the coded proteins and the free folding energy of mRNAs. This additional information, which seems to be necessary to determine the 3D structure of coding nucleic acids as well as the coded proteins, is known as the Proteomic Code and mRNA Assisted Protein Folding.     

CDM-系列开窗导流式催化精馏模块在C4/C5醚化等反应中的工业应用

CDM-系列开窗导流式催化精馏模块具有优异的"催化反应"和"组分分离"双重功能,综合性能优于催化蒸馏组件CDP,是其升级换代产品。可应用于甲基叔丁基醚、轻汽油醚化、异丁烯叠合和叔丁醇脱水等工艺中,主要介绍CDM-系列开窗导流式催化精馏模块产品特点及在工业装置中的应用情况。     

软模板法制备多级孔ZSM-5分子筛的研究进展

相比传统ZSM-5分子筛,多级孔ZSM-5分子筛具有空间位阻小、传质效率高、焦炭少等特点,近年来在分子筛领域应用广泛。多级孔分子筛通常可用后处理法和模板剂法制备,相比后处理法,模板剂法能更好地控制介孔的结构和孔道尺寸。概述了采用传统表面活性剂、两亲性的有机硅烷、双功能多季铵盐表面活性剂及高分子聚合物等软模板法合成多级孔ZSM-5分子筛的研究进展。分析不同软模板剂的特点和作用机理,阐述了合成后分子筛的结构特点及催化性能等。指出在今后的研究中,可以设计价格较低的新型功能化模板剂,优化合成过程,致力于在理解合成机理的前提下,寻找操作简单、绿色环保的合成路线,并将其推行到实际工业生产中。     

Effects of Aluminium Contamination on the Nervous System of Freshwater Aquatic Vertebrates: A Review

Aluminium (Al) is the most common natural metallic element in the Earth’s crust. It is released into the environment through natural processes and human activities and accumulates in aquatic environments. This review compiles scientific data on the neurotoxicity of aluminium contamination on the nervous system of aquatic organisms. More precisely, it helps identify biomarkers of aluminium exposure for aquatic environment biomonitoring in freshwater aquatic vertebrates. Al is neurotoxic and accumulates in the nervous system of aquatic vertebrates, which is why it could be responsible for oxidative stress. In addition, it activates and inhibits antioxidant enzymes and leads to changes in acetylcholinesterase activity, neurotransmitter levels, and in the expression of several neural genes and nerve cell components. It also causes histological changes in nerve tissue, modifications of organism behaviour, and cognitive deficit. However, impacts of aluminium exposure on the early stages of aquatic vertebrate development are poorly described. Lastly, this review also poses the question of how accurate aquatic vertebrates (fishes and amphibians) could be used as model organisms to complement biological data relating to the developmental aspect. This “challenge” is very relevant since freshwater pollution with heavy metals has increased in the last few decades.     

Possible Alterations in ��-Synuclein, the Non-Amyloidogenic Homologue of ��-Synuclein, during Progression of Sporadic ��-Synucleinopathies

α-Synucleinopathies are neurodegenerative disorders that are characterized by progressive decline of motor and non-motor dysfunctions. α-Synuclein (αS) has been shown to play a causative role in neurodegeneration, but the pathogenic mechanisms are still unclear. Thus, there are no radical therapies that can halt or reverse the disease’s progression. β-Synuclein (βS), the non-amyloidogenic homologue of αS, ameliorates the neurodegeneration phenotype of αS in transgenic (tg) mouse models, as well as in cell free and cell culture systems, which suggests that βS might be a negative regulator of neurodegeneration caused by αS, and that “loss of function” of βS might be involved in progression of α-synucleinopathies. Alternatively, it is possible that “toxic gain of function” of wild type βS occurs during the pathogenesis of sporadic α-synucleinopathies, since tg mice expressing dementia with Lewy bodies-linked P123H βS develop progressive neurodegeneration phenotypes, such as axonal pathology and dementia. In this short review, we emphasize the aspects of “toxic gain of function” of wild type βS during the pathogenesis of sporadic α-synucleinopathies.     

Advances Towards Synthetic Machines at the Molecular and Nanoscale Level

The fabrication of increasingly smaller machines to the nanometer scale can be achieved by either a “top-down” or “bottom-up” approach. While the former is reaching its limits of resolution, the latter is showing promise for the assembly of molecular components, in a comparable approach to natural systems, to produce functioning ensembles in a controlled and predetermined manner. In this review we focus on recent progress in molecular systems that act as molecular machine prototypes such as switches, motors, vehicles and logic operators.