There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

基礎講座 電気泳動(Electrophoresis)

Yuming Yang,†,§ Qiang Zhao,‡,§ Wei Feng,† and Fuyou Li*,† †Department of Chemistry and State Key Laboratory of Molecular Engineering of Polymers and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China ‡Key Laboratory for Organic Electronics and Information Displays (KLOEID) and Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210046, P. R. China.

Luminescent chemodosimeters for bioimaging.

Surface-enhanced Raman scattering (SERS) has become a mature vibrational spectroscopic technique during the last decades and the number of applications in the chemical, material, and in particular life sciences is rapidly increasing. This Review explains the basic theory of SERS in a brief tutorial and-based on original results from recent research-summarizes fundamental aspects necessary for understanding SERS and provides examples for the preparation of plasmonic nanostructures for SERS. Chemical applications of SERS are the centerpiece of this Review. They cover a broad range of topics such as catalysis and spectroelectrochemistry, single-molecule detection, and (bio)analytical chemistry.

Surface-enhanced Raman spectroscopy: concepts and chemical applications.

Molecular imprinting technology (MIT), often described as a method of making a molecular lock to match a molecular key, is a technique for the creation of molecularly imprinted polymers (MIPs) with tailor-made binding sites complementary to the template molecules in shape, size and functional groups. Owing to their unique features of structure predictability, recognition specificity and application universality, MIPs have found a wide range of applications in various fields. Herein, we propose to comprehensively review the recent advances in molecular imprinting including versatile perspectives and applications, concerning novel preparation technologies and strategies of MIT, and highlight the applications of MIPs. The fundamentals of MIPs involving essential elements, preparation procedures and characterization methods are briefly outlined. Smart MIT for MIPs is especially highlighted including ingenious MIT (surface imprinting, nanoimprinting, etc.), special strategies of MIT (dummy imprinting, segment imprinting, etc.) and stimuli-responsive MIT (single/dual/multi-responsive technology). By virtue of smart MIT, new formatted MIPs gain popularity for versatile applications, including sample pretreatment/chromatographic separation (solid phase extraction, monolithic column chromatography, etc.) and chemical/biological sensing (electrochemical sensing, fluorescence sensing, etc.). Finally, we propose the remaining challenges and future perspectives to accelerate the development of MIT, and to utilize it for further developing versatile MIPs with a wide range of applications (650 references).

http://ir.yic.ac.cn/bitstream/133337/17045/1/Molecular%20imprinting%20perspectives%20and%20applications.pdf

Molecular imprinting: perspectives and applications

Molecular imprinting technology (MIT) concerns formation of selective sites in a polymer matrix with the memory of a template. Recently, molecularly imprinted polymers (MIPs) have aroused extensive attention and been widely applied in many fields, such as solid-phase extraction, chemical sensors and artificial antibodies owing to their desired selectivity, physical robustness, thermal stability, as well as low cost and easy preparation. With the rapid development of MIT as a research hotspot, it faces a number of challenges, involving biological macromolecule imprinting, heterogeneous binding sites, template leakage, incompatibility with aqueous media, low binding capacity and slow mass transfer, which restricts its applications in various aspects. This critical review briefly reviews the current status of MIT, particular emphasis on significant progresses of novel imprinting methods, some challenges and effective strategies for MIT, and highlighted applications of MIPs. Finally, some significant attempts in further developing MIT are also proposed (236 references).

http://ir.yic.ac.cn/bitstream/133337/4853/1/Recent%20advances%20in%20molecular%20imprinting%20technology%20current%20status%2c%20challenges%20and%20highlighted%20applications.pdf

Recent advances in molecular imprinting technology: current status, challenges and highlighted applications

CONTENTS 1. Introduction 1.1. Fundamental Theory of Surface-Enhanced Raman Scattering 1.2. Optical Properties of SERS Tags 2. Synthesis of SERS Tags 2.1. Noble Metal Nanosubstrates 2.1.1. Single Particle-Based SERS Substrates 2.1.2. Nanoparticle Cluster-Based Substrates 2.2. Raman Reporter Molecules 2.2.1. Selection Principles and Reporter Types 2.2.2. Self-Assembled Monolayer Coverage Strategy 2.3. Surface Coating for Protection 2.3.1. Biomolecule Coating 2.3.2. Polymer Coating 2.3.3. Liposome Coating 2.3.4. Silica Coating 2.4. Attachment of Targeting Molecules 3. Bioanalysis Applications 3.1. Ionic and Molecular Detection 3.2. Pathogen Detection 3.3. Live-Cell Imaging 3.3.1. Cancer Marker Detection 3.3.2. Intercellular Microenvironment Sensing 3.4. Tissue SERS Imaging 3.5. In Vivo SERS Imaging 4. Challenges and Perspectives 4.1. Reproducible Signal of SERS Tags 4.1.1. Precisely Controlled Hot Spots for Nanosubstrates 4.1.2. Calibration of SERS Intensities and Enhancements 4.2. Improving Multiplexing Capability 4.3. Reduced Size for Subcellular Imaging 4.4. Development of Multifunctional Nanoplatforms 4.4.1. Magnetic SERS Dots 4.4.2. Multimodal Imaging Dots 4.4.3. SERS Tag-Based Therapeutic Systems 4.5. Biocompatibility 5. Conclusions and Remarks

SERS Tags: Novel Optical Nanoprobes for Bioanalysis

Surgical resection of solid tumors is currently the gold standard and preferred therapeutic strategy for cancer. Chemotherapy drugs also make a significant contribution by inhibiting the rapid growth of tumor cells and these two approaches are often combined to enhance treatment efficacy. However, surgery and chemotherapy inevitably lead to severe side effects and high systemic toxicity, which in turn results in poor prognosis. Precision medicine has promoted the development of treatment modalities that are developed to specifically target and kill tumor cells. Advances in in vivo medical imaging for visualizing tumor lesions can aid diagnosis, facilitate surgical resection, investigate therapeutic efficacy, and improve prognosis. In particular, the modality of fluorescence imaging has high specificity and sensitivity and has been utilized for medical imaging. Therefore, there are great opportunities for chemists and physicians to conceive, synthesize, and exploit new chemical probes that can image tumors and release chemotherapy drugs in vivo. This review focuses on small molecular ligand-targeted fluorescent imaging probes and fluorescent theranostics, including their design strategies and applications in clinical tumor treatment. The progress in chemical probes described here suggests that fluorescence imaging is a vital and rapidly developing field for interventional surgical imaging, as well as tumor diagnosis and therapy.

/pdf/fluorescent-chemical-probes-for-accurate-tumor-diagnosis-and-3j5p8i5h85.pdf

Fluorescent chemical probes for accurate tumor diagnosis and targeting therapy

As defined by the European Commission, nanomaterial is a natural, incidental or manufactured material containing particles in an unbound state or as an aggregate or agglomerate in which ≥ 50% of the particles in the number size distribution have one or more external dimensions in the size range 1 to 100 nm. In specific cases and where warranted by concerns for the environment, health, safety or competition, the number size distribution threshold of 50% may be replaced with a threshold between 1 and 50%.1 Engineered nanomaterials (ENMs) refer to man-made nanomaterials. Materials in the nanometer range often possess unique physical, optical, electronic, and biological properties compared with larger particles, such as the strength of graphene,2 the electronic properties of carbon nanotubes (CNTs),3 the antibacterial activity of silver nanoparticles4 and the optical properties of quantum dots (QDs).5 The unique and advanced properties of ENMs have led to a rapid increase in their application. These applications include aerospace and airplanes, energy, architecture, chemicals and coatings, catalysts, environmental protection, computer memory, biomedicine and consumer products. Driven by these demands, the worldwide ENM production volume in 2016 is conservatively estimated in a market report by Future Markets to be 44,267 tons or ≥ $5 billion.6

As the production and applications of ENMs rapidly expand, their environmental impacts and effects on human health are becoming increasingly significant.7 Due to their small sizes, ENMs are easily made airborne.8 However, no accurate method to quantitatively measure their concentration in air currently exists. A recently reported incident of severe pulmonary fibrosis caused by inhaled polymer nanoparticles in seven female workers obtained much attention.9 In addition to the release of ENM waste from industrial sites, a major release of ENMs to environmental water occurs due to home and personal use of appliances, cosmetics and personal products, such as shampoo and sunscreen.10 Airborne and aqueous ENMs pose immediate danger to the human respiratory and gastrointestinal systems. ENMs may enter other human organs after they are absorbed into the bloodstream through the gastrointestinal or respiratory systems.11,12 Furthermore, ENMs in cosmetics and personal care products, such as lotion, sunscreen and shampoo may enter human circulation through skin penetration.13 ENMs are very persistent in the environment and are slowly degraded. The dissolved metal ions from ENMs can also revert back to nanoparticles under natural conditions.14 ENMs are stored in plants, microbes and animal organs and can be transferred and accumulated through the food chain.15,16 In addition to the accidental entry of ENMs into human and biological systems, ENMs are also purposefully injected into or enter humans for medicinal and diagnostic purposes.17 Therefore, interactions of ENMs with biological systems are inevitable.

In addition to engineered nanomaterials, there are also naturally existing nanomaterials such as proteins and DNA molecules, which are key components of biological systems. These materials, combined with lipids and organic and inorganic small molecules, form the basic units of living systems –cells.18 To elucidate how nanomaterials affect organs and physiological functions, a thorough understanding of how nanomaterials perturb cells and biological molecules is required (Figure 1). Rapidly accumulating evidence indicates that ENMs interact with the basic components of biological systems, such as proteins, DNA molecules and cells.19-21 The driving forces for such interactions are quite complex and include the size, shape and surface properties (e.g., hydrophobicity, hydrogen-bonding capability, pi-bonds and stereochemical interactions) of ENMs.22-25



Figure 1

Interactions of nanoparticles with biological systems at different levels. Nanoparticles enter the human body through various pathways, reaching different organs and contacting tissues and cells. All of these interactions are based on nanoparticle-biomacromolecule ...



Evidence also indicates that chemical modifications on a nanoparticle’s surface alter its interactions with biological systems.26-28 These observations not only support the hypothesis that basic nano-bio interactions are mainly physicochemical in nature but also provide a powerful approach to controlling the nature and strength of a nanoparticle’s interactions with biological systems. Practically, a thorough understanding of the fundamental chemical interactions between nanoparticles and biological systems has two direct impacts. First, this knowledge will encourage and assist experimental approaches to chemically modify nanoparticle surfaces for various industrial or medicinal applications. Second, a range of chemical information can be combined with computational methods to investigate nano-biological properties and predict desired nanoparticle properties to direct experiments.29-31

The literature regarding nanoparticle-biological system interactions has increased exponentially in the past decade (Figure 2). However, a mechanistic understanding of the chemical basis for such complex interactions is still lacking. This review intends to explore such an understanding in the context of recent publications.



Figure 2

An analysis of literature statistics indicates growing concern for the topics that are the focus of this review. The number of publications and citations were obtained using the keywords “nanoparticles” and “biological systems” ...



A breakthrough technology cannot prosper without wide acceptance from the public and society; that is, it must pose minimal harm to human health and the environment. Nanotechnology is now facing such a critical challenge. We must elucidate the effects of ENMs on biological systems (such as biological molecules, human cells, organs and physiological systems). Accumulating experimental evidence suggests that nanoparticles interact with biological systems at nearly every level, often causing unwanted physiological consequences. Elucidating these interactions is the goal of this review. This endeavor will help regulate the proper application of ENMs in various products and their release into the environment. A more significant mission of this review is to direct the development of “safe-by-design” ENMs, as their demands for and applications continue to increase.

Lingxin Chen

Papers

Molecular imprinting: perspectives and applications

Recent advances in molecular imprinting technology: current status, challenges and highlighted applications

SERS Tags: Novel Optical Nanoprobes for Bioanalysis

Fluorescent chemical probes for accurate tumor diagnosis and targeting therapy

Chemical Basis of Interactions Between Engineered Nanoparticles and Biological Systems