Les systèmes vivants : une source d’inspiration pour les microsystèmes et les capteurs biomédicaux

Living beings are inventing, testing, improving new concepts, solutions and devices from hundred millions years. These living systems are able of self-feeding, they take their energy for the environment and also, they are able of reproduction, adaptation and self-repairing. Living beings as birds, butterflies, sharks and dolphins have optimized flight and swimming and their surface for moving with the lowest energy cost. The golf ball, the wings of aircraft, ships and submarines… are now inspired by the Nature's aero- and hydrodynamism. Our organs and tissues are under the control of millions of microsensors, which measure physical, chemical, mechanical… parameters and are associated to microactuators. This distributed intelligence is present even in the structure of living beings. The wing of fly or dragon fly and also bones have extraordinary characteristics of mechanical resistance and lightness and their complex structure is designed so that at any place there is exactly and appropriate quantities of matter with the good orientation and the smallest weight. The new materials, micro- and nanotechnologies, signal processing, the progress in chemistry and optics… allow us to understand and also to design and build at the scale and size of Nature, using its concepts and taking advantage of the human technologies. It is not always possible to copy directly living beings and their solutions; nature does not give us blue print “ready to copy”. We have to analyze the content of the “huge data bank” of living beings for the adaptation of our technologies. Miniaturization, intelligence, low energy, recycling, low cost, high reliability are the main qualities of “bioinspired devices”. They fit exactly with the needs of modern users. The multidisciplinary and the bioinspired approach have to link engineers, scientists and industrials for taking real benefits.     

Utilization of adenovirus vectors for multiple gene transfer applications

Mammalian viruses have evolved over millions of years to achieve a single goal, namely to rapidly enter a host mammalian cell, in order to achieve virus propagation. In so doing, these biologic parasites have acquired the molecular tools to rapidly and efficiently deliver their own nucleic acids into the nucleus of the host cell. The human adenovirus is one of the best studied of these parasites. As such the adenovirus has been re-engineered to allow it to be used as a tool to allow researchers to deliver desired nucleic acid sequences into a large variety of cell targets, both in tissue culture systems, as well as directly into living animals. Adenovirus based gene transfer systems can overcome most of the problems inherent to high efficiency gene transfer, and perform in a fashion that in many ways cannot be matched by most other currently utilized gene transfer systems. This article will attempt to summarize the multiple attributes of this widely utilized gene delivery system.     

基于酿酒酵母的大片段DNA组装与转移技术进展*

DNA组装与转移技术是合成生物学的核心使能技术之一,生命体设计改造的复杂度不断提升,使得对大片段DNA组装与转移技术的需求也日益旺盛。小片段DNA的组装与转移技术目前已经比较成熟,大片段DNA由于其分子量大、易断裂,使得体外操作繁琐且效率低下。聚焦酿酒酵母体内组装和转移的技术进展,详细介绍了基于酿酒酵母一次组装和迭代组装的不同方法,并从导入与导出的角度介绍了大片段DNA的转移技术,便于研究者更好地理解和选择酿酒酵母体内组装与转移技术。此外,还展望了将酿酒酵母开发为大片段DNA组装与转移通用平台实现更多物种基因组大尺度设计改造的愿景。     

Assay concordance between SPA and TR-FRET in high-throughput screening

High-throughput screening (HTS) of large chemical libraries has become the main source of new lead compounds for drug development. Several specialized detection technologies have been developed to facilitate the cost- and time-efficient screening of millions of compounds. However, concerns have been raised, claiming that different HTS technologies may produce different hits, thus limiting trust in the reliability of HTS data. This study was aimed to investigate the reliability of the authors most frequently used assay techniques: scintillation proximity assay (SPA) and homogeneous time-resolved fluorescence resonance energy transfer (TR-FRET). To investigate the data concordance between these 2 detection technologies, the authors screened a large subset of the Schering compound library consisting of 300,000 compounds for inhibitors of a nonreceptor tyrosine kinase. They chose to set up this study in realistic HTS scale to ensure statistical significance of the results. The findings clearly demonstrate that the choice of detection technology has no significant impact on hit finding, provided that assays are biochemically equivalent. Data concordance is up to 90%. The little differences in hit findings are caused by threshold setting but not by systematic differences between the technologies. The most significant difference between the compared techniques is that in the SPA format, more false-positive primary hits were obtained.     

Cancer drug resistance: A fleet to conquer

Cancer is a disease that claims millions of lives each year across the world. Despite advancement in technologies and therapeutics for treating the disease, these modes are often found to turn ineffective during the course of treatment. The resistance against drugs in cancer patients stems from multiple factors, which constitute genetic heterogeneity like gene mutations, tumor microenvironment, exosomes, miRNAs, high rate of drug efflux from cells, and so on. This review attempts to collate all such known and reported factors that influence cancer drug resistance and may help researchers with information that might be useful in developing better therapeutics in near future to enable better management of several cancers across the world.     

Origin and evolution of chloroplast group I introns in lichen algae

The history of group I introns is characterized by repeated horizontal transfers, even among phylogenetically distant species. The symbiogenetic thalli of lichens are good candidates for the horizontal transfer of genetic material among distantly related organisms, such as fungi and green algae. The main goal of this study was to determine whether there were different trends in intron distribution and properties among Chlorophyte algae based on their phylogenetic relationships and living conditions. Therefore, we investigated the occurrence, distribution and properties of group I introns within the chloroplast LSU rDNA in 87 Chlorophyte algae including lichen and free‐living Trebouxiophyceae compared to free‐living non‐Trebouxiophyceae species. Overall, our findings showed that there was high diversity of group I introns and homing endonucleases (HEs) between Trebouxiophyceae and non‐Trebouxiophyceae Chlorophyte algae, with divergence in their distribution patterns, frequencies and properties. However, the differences between lichen Trebouxiophyceae and free‐living Trebouxiophyceae were smaller. An exception was the cL2449 intron, which was closely related to ω elements in yeasts. Such introns seem to occur more frequently in lichen Trebouxiophyceae compared to free‐living Trebouxiophyceae. Our data suggest that lichenization and maintenance of lichen symbiosis for millions of years of evolution may have facilitated horizontal transfers of specific introns/HEs between symbionts. The data also suggest that sequencing of more chloroplast genes harboring group I introns in diverse algal groups may help us to understand the group I intron/HE transmission process within these organisms.     

NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data

Third‐generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long‐read sequences. This is not only advantageous for genome sequencing projects, but also advantageous for amplicon‐based high‐throughput sequencing experiments, such as DNA barcoding. However, the relatively high error rates associated with these technologies still pose challenges for generating high‐quality consensus sequences. Here, we present NGSpeciesID, a program which can generate highly accurate consensus sequences from long‐read amplicon sequencing technologies, including ONT and PacBio. The tool includes clustering of the reads to help filter out contaminants or reads with high error rates and employs polishing strategies specific to the appropriate sequencing platform. We show that NGSpeciesID produces consensus sequences with improved usability by minimizing preprocessing and software installation and scalability by enabling rapid processing of hundreds to thousands of samples, while maintaining similar consensus accuracy as current pipelines.     

新基因起源：从自然进化到人工设计

生命体系历经40多亿年的自然进化,创造了无数丰富多彩的功能基因,保障了生命体系的传承与繁荣。然而生命体系的自然进化历程极其缓慢,新的功能基因产生需要数百万年时间,无法满足快速发展的工业生产需求。利用合成生物学技术,研究人员可以依据已知的酶催化机理和蛋白质结构进行全新的基因设计与合成,按照工业生产需求快速创造全新的蛋白质催化剂,实现各种自然界生物无法催化的生物化学反应。尽管新基因设计技术展现了激动人心的应用前景,但是目前该技术还存在设计成功率不高、酶催化活性较低、合成成本较高等科技挑战。未来随着合成生物学技术的快速发展,设计、改造、合成和筛选等技术将融合为一体,为新基因设计与创建带来全新的发展机遇。     

Selective DNA amplification from complex genomes using universal double-sided adapters

There is a rapidly developing need for new technologies to amplify millions of different targets from genomic DNA for high throughput genotyping and population gene-sequencing from diverse species. Here we describe a novel approach for the specific selection and amplification of genomic DNA fragments of interest that eliminates the need for costly and time consuming synthesis and testing of potentially millions of amplicon-specific primers. This technique relies upon Type IIs restriction enzyme digestion of genomic DNA and ligation of the fragments to double-sided adapters to form closed-circular DNA molecules. The novel use of double-sided adapters, assembled through the combinatorial use of two small universal sets of oligonucleotide building blocks, provides greater selection capacity by utilizing both sides of the adapter in a sequence-specific ligation event. As demonstrated, formation of circular structures results in protection of the desired molecules from nuclease treatment and enables a level of selectivity high enough to isolate single, or multiple, pre-defined fragments from the human genome when digested at over five million sites. Priming sites incorporated into the adapter allows the utilization of a common pair of primers for the amplification of any adapter-captured DNA fragment of interest.     

FRET技术在受体信号转导研究中的应用

细胞信号传导是细胞生物学方面的重要内容之一,涉及生命过程的各个方面,包括生长、分化发育、增殖、凋亡、迁移等等,对维持细胞功能及机体生存至关重要。目前对细胞信号转导研究的技术手段多种多样,其中荧光共振能量转移技术（FRET）是研究细胞信号转导较为常用的一种技术,可以实现活细胞内蛋白质之间相互作用的实时检测。本文中我们以受体酪氨酸激酶为例,介绍FRET技术在受体介导细胞信号传导中的应用及进展情况。     

Analytical study on bioheat transfer problems with spatial or transient heating on skin surface or inside biological bodies

Several closed form analytical solutions to the bioheat transfer problems with space or transient heating on skin surface or inside biological bodies were obtained using Green's function method. The solutions were applied to study several selected typical bioheat transfer processes, which are often encountered in cancer hyperthermia, laser surgery, thermal comfort analysis, and tissue thermal parameter estimation. Thus a straightforward way to quantitatively interpret the temperature behavior of living tissues subject to constant, sinusoidal, step, point or stochastic heatings etc. both in volume and on boundary were established. Further solution to the three-dimensional bioheat transfer problems was also given to illustrate the versatility of the present method. Implementations of this study to the practical problems were addressed.     

Biological laser printing of genetically modified Escherichia coli for biosensor applications

One of the primary requirements of cell- or tissue-based sensors is the placement of cells and cellular material at or near the sensing elements of the device. The ability to achieve precise, reproducible and rapid placement of cells is the focus of this study. We have developed a technique, biological laser printing or BioLP, which satisfies these requirements and has advantages over current technologies. BioLP is capable of rapidly depositing patterns of active biomolecules and living cells onto a variety of material surfaces. Unlike ink jet or manual spotting techniques, this process delivers small volume (nl to fl) aliquots of biomaterials without the use of an orifice, thus eliminating potential clogging issues and enabling diverse classes of biomaterials to be deposited. This report describes the use of this laser-based printing method to transfer genetically-modified bacteria capable of responding to various chemical stressors onto agar-coated slides and into microtiter plates. The BioLP technology enables smaller spot sizes, increased resolution, and improved reproducibility compared to related technologies.     

Homodimerization of Amyloid Precursor Protein at the Plasma Membrane: A homoFRET Study by Time-Resolved Fluorescence Anisotropy Imaging

Classical FRET (Förster Resonance Energy Transfer) using two fluorescent labels (one for the donor and another one for the acceptor) is not efficient for studying the homodimerization of a protein as only half of the homodimers formed can be identified by this technique. We thus resorted to homoFRET detected by time-resolved Fluorescence Anisotropy IMaging (tr-FAIM). To specifically image the plasma membrane of living cells, an original combination of tr-FAIM and Total Internal Reflection Fluorescence Lifetime Imaging Microscope (TIRFLIM) was implemented. The correcting factor accounting for the depolarization due to the high numerical aperture (NA) objective, mandatory for TIRF microscopy, was quantified on fluorescein solutions and on HEK293 cells expressing enhanced Green Fluorescence Protein (eGFP). Homodimerization of Amyloid Precursor Protein (APP), a key mechanism in the etiology of Alzheimer’s disease, was measured on this original set-up. We showed, both in epifluorescence and under TIRF excitation, different energy transfer rates associated with the homodimerization of wild type APP-eGFP or of a mutated APP-eGFP, which forms constitutive dimers. This original set-up thus offers promising prospects for future studies of protein homodimerization in living cells in control and pathological conditions.     

The westernmost tarsier: A new genus and species from the Miocene of Pakistan

As the closest living sister group of anthropoids, tarsiers (Family Tarsiidae) are an important group in primate evolution. However, their fossil record is poor: only four species have been described, two from the Eocene of China and two from the Miocene of Thailand. All are from outside the range of the living species, which occur only on islands off Southeast Asia. Here, we describe a new fossil tarsier from Pakistan, a significant range extension. This record consists of two lower molars, an upper molar, and a lower premolar found in the Miocene Manchar Formation (∼18–16 Ma [millions of years ago]) of Sindh Province, southern Pakistan. The Pakistani tarsier is morphologically distinct from all living and fossil tarsiers, but most similar to the middle Miocene Thai species Tarsius thailandicus. Though living tarsiers have traditionally been classified in a single genus, a recent revision proposed a division into three genera, which is strongly supported by molecular data. The Pakistani species is not referable to any of these genera, and we create for it and T. thailandicus a new tarsiid genus. This discovery broadens our understanding of the geographic range and morphological diversity of Miocene tarsiers and helps to put the living tarsiers into their evolutionary context.     

Study of kinetic parameters of singlet molecular oxygen in aqueous porphyrin solutions. Effect of detergents and the quencher sodium azide

The kinetic parameters of porphyrin-photosensitized formation and deactivation of singlet molecular oxygen (1O2) and their dependence on the concentration of the 1O2 quencher sodium azide were investigated in air-saturated water, ethanol, and aqueous micellar solutions of detergents using time-resolved measurements of oxygen phosphorescence under pulsed laser excitation. The lifetimes of 1O2 formation and deactivation and the rate constants of 1O2 quenching by sodium azide were determined. It was shown that, with no azide in the solutions, the rise in phosphorescence intensity after the laser flash corresponded to the kinetics of energy transfer from the porphyrin triplet molecules to oxygen, while the decay kinetics corresponded to the kinetics of 1O2 deactivation. In the presence of detergent, a considerable increase in the 1O2 lifetime was observed, which is likely due to the localization of 1O2 molecules mostly in lipophilic micelles and not in the water phase. If relatively high azide concentrations were used, the lifetime of the porphyrin triplet state did not change but the 1O2 lifetime decreased to values similar to those in living cells. In this case, the inversion of the phosphorescence kinetic phases was observed. The rise corresponded to 1O2 deactivation, and the decay, to the energy transfer from triplet porphyrin to oxygen. The data suggest that, in living cells, 1O2 molecules are also located mainly in lipophilic structures and the 1O2 lifetime determines the kinetics of the phosphorescence rise after the laser pulse.     

Finding sRNA generative locales from high-throughput sequencing data with NiBLS

Background  

Next-generation sequencing technologies allow researchers to obtain millions of sequence reads in a single experiment. One important use of the technology is the sequencing of small non-coding regulatory RNAs and the identification of the genomic locales from which they originate. Currently, there is a paucity of methods for finding small RNA generative locales.     

中国西藏拉托唐古墓地古代居民线粒体全基因组研究

目前青藏高原高海拔地区古DNA研究匮乏。拉托唐古墓地位于青藏高原西南高海拔区域,本文对该墓地出土距今约700年的人骨进行古DNA提取,捕获了高质量线粒体全基因组数据,结合东亚线粒体基因组数据库,运用遗传统计方法开展分析。研究结果表明,距今3000年以内青藏高原西南部人群的遗传历史具有连续性,距今700年左右的拉托唐古墓地居民与距今3150-1250年的古代尼泊尔居民以及现代中国西藏居民母系遗传关系较近,且他们都具有共同的M9a1a1c1b1a单倍群。对M9a1a1c1b1a单倍群的深入研究发现,距今10930-5150年期间青藏高原可能发生了人口扩张事件。以上结果为我们了解古代青藏高原高海拔地区人群遗传历史提供了重要信息。     

Advancements in transfection technologies for Plasmodium

Malaria is a global problem that affects millions of people annually. A relatively poor understanding of the malaria parasite biology has hindered vaccine and drug development against this disease. Robust methods for genetic analyses in Plasmodium have been lacking due to the difficulties in its genetic manipulation. Introduction of transfection technologies laid the foundation for genetic dissection of Plasmodium and recent years have seen the development of novel tools for genetic manipulation that will help us delineate the intriguing biology of this parasite. This review focuses on such recent advances in transfection technologies for Plasmodium that have improved our ability to carry out more thorough genetic analyses of the biology of the malaria parasite.