Xuemin Xu

Bio: Xuemin Xu is an academic researcher from Shanghai Jiao Tong University. The author has contributed to research in topics: Geology & Medicine. The author has an hindex of 1, co-authored 1 publications receiving 24 citations.

High‐resolution imaging and nano‐manipulation of biological structures on surface

Abstract: In this mini-review we discuss our recent findings on imaging and manipulation of biological macromolecular structures by atomic force microscopy (AFM). In the first part of this review, we focus on high-resolution imaging of selected biological samples. AFM images of membrane proteins have revealed detailed conformational features related to identifiable biological functions. Different self-assembling behaviors of short peptides into supramolecular structures on various substrates under controlled environmental conditions have been systematically studied with AFM imaging. In the second part, we present a novel nano-manipulation technique for manipulating, isolating, amplifying, and sequencing of individual DNA molecules, which may find unique applications in the analysis of difficult sequence structures. Finally, we discuss how to characterize the elasticity of individual biomolecules and live cells. These results demonstrate that not only the high resolution capacity of the AFM is suited to resolve certain biological questions, but can also be applied to single molecule isolation and biomechanical analysis with its unique advantages. Microsc. Res. Tech. 74: 614-626, 2011. (C) 2010 Wiley-Liss, Inc.

Geochemical Characteristics and Significance of Organic Matter in Hydrate-Bearing Sediments from Shenhu Area, South China Sea

Abstract: Rock-Eval pyrolysis and the biomarker composition of organic matter were systematically studied in hydrate-bearing sediments from the Shenhu area, South China Sea. The n-alkane distribution patterns revealed that the organic matter in the sediments appeared to originate from mixed sources of marine autochthonous input, terrestrial higher plants, and ancient reworked organic matter. The low total organic carbon contents (average < 0.5%) and the low hydrogen index (HI, <80 mg HC/g TOC) suggested the poor hydrocarbon-generation potential of the deposited organic matter at a surrounding temperature of <20 °C in unconsolidated sediments. The abnormally high production index and the fossil-originated unresolved complex mixture (UCM) accompanied by sterane and hopane of high maturity indicated the contribution of deep hydrocarbon reservoirs. Preliminary oil-to-source correlation for the extracts implied that the allochthonous hydrocarbons in the W01B and W02B sediments might have originated from the terrestrial source rocks of mature Enping and Wenchang formations, while those of W03B seem to be derived from more reduced and immature marine source rocks such as the Zhuhai formation. The results of the organic extracts supported the previous identification of source rocks based on the isotopic composition of C2+ hydrate-bound gases. The biomarker of methanogens, squalane, was recognized in the sediments of this study, possibly suggesting the generation of secondary microbial gases which are coupled with the biodegradation of the deep allochthonous hydrocarbons.

Microbial communities associated with thermogenic gas hydrate-bearing marine sediments in Qiongdongnan Basin, South China Sea

Abstract: Biogenic and thermogenic gas are two major contributors to gas hydrate formation. Methane hydrates from both origins may have critical impacts on the ecological properties of marine sediments. However, research on microbial diversity in thermogenic hydrate-containing sediments is limited. This study examined the prokaryotic diversity and distributions along a sediment core with a vertical distribution of thermogenic gas hydrates with different occurrences obtained from the Qiongdongnan Basin by Illumina sequencing of 16S rRNA genes as well as molecular and geochemical techniques. Here, we show that gas hydrate occurrence has substantial impacts on both microbial diversity and community composition. Compared to the hydrate-free zone, distinct microbiomes with significantly higher abundance and lower diversity were observed within the gas hydrate-containing layers. Gammaproteobacteria and Actinobacterota dominated the bacterial taxa in all collected samples, while archaeal communities shifted sharply along the vertical profile of sediment layers. A notable stratified distribution of anaerobic methanotrophs shaped by both geophysical and geochemical parameters was also determined. In addition, the hydrate-free zone hosted a large number of rare taxa that might perform a fermentative breakdown of proteins in the deep biosphere and probably respond to the hydrate formation.

Cellular interactions of doxorubicin-loaded DNA-modified halloysite nanotubes

Abstract: Halloysite nanotube (HNT)-based supramolecular complexes are synthesized and evaluated with respect to their cytotoxicity and effects on cellular structures. As HNTs are water-insoluble, DNA is applied for wrapping the surface of HNTs to enhance their water-dispersibility. To investigate the potential of DNA-wrapped HNTs (HD) as a promising drug delivery carrier, doxorubicin (DOX) is introduced as a model anticancer agent and loaded onto HD. The DOX-loaded, DNA-wrapped HNTs (HDD) show sustained DOX release over two weeks without initial burst of DOX indicating delayed DOX release inside cells. In addition, effects of DNA-wrapped HNTs (HD) or HDD on the cytoskeleton organization of A549 cells are studied by visualizing the distribution of F-actin filaments using confocal laser scanning microscopy, and cellular morphological changes are observed by scanning electron microscopy and scanning ion conductance microscopy.

Seeing is believing: atomic force microscopy imaging for nanomaterial research

Abstract: The research and development of nanotechnology has led to materials science and engineering entering the “nanomaterial era”. It is pivotal for analyzing the physicochemical properties of nanomaterials for new nanotechnological instruments to be developed. Over the past three decades, atomic force microscopy (AFM), as a powerful nanotechnological imaging tool, has provided many imaging modes for analyzing nanomaterial properties such as the topography, elasticity, adhesion, friction, electrical properties, and magnetism of the materials. The focus of this review is on the development of AFM imaging observation tools and methods for nanomaterial research. First, AFM and nanomaterials are briefly introduced. Then, AFM imaging techniques for nanomaterial research are comprehensively summarized. Finally, the advantages and disadvantages of AFM imaging techniques for nanomaterial research are discussed. This review will provide comprehensive information of AFM imaging techniques for materials scientists and engineers.

Tip-induced micropatterning of silk fibroin protein using in situ solution atomic force microscopy.

Abstract: Silk fibroin (SF) is a promising candidate for a variety of application in the fields of tissue engineering, drug delivery, and biomedical optics. Recent research has already begun to explore the construction of nano- and micropatterned SF films under ambient environment. The structure and biocompatibility of SF are dependent on SF state (solution or solid) and the method of drying the SF solution to prepare various biomaterials such as films, sponges, and fibers. Therefore, it is important to explore the construction of SF nano- and micropatterns under aqueous solution. This paper reports a novel application of atomic force microscopy (AFM) under liquid for direct deposition of the relatively hydrophobic protein SF onto hydrophilic mica. We demonstrate that the AFM tip, in either the contact or the tapping mode, can fabricate SF micropatterns on mica with controlled surface topography. We show that the deposition process requires a mechanical force-induced SF sol–gel transition followed by a transfer to ...

Nanoimaging of food proteins by atomic force microscopy. Part I: Components, imaging modes, observation ways, and research types

Abstract: s Background Since atomic force microscopy (AFM) was developed in 1985, AFM has become an important nanotech tool to analyze the morphological properties and mechanical properties of proteins. In the past three decades, many food scientists used AFM to analyze food proteins and to comprehensively understand the relationship between the structure and the function of food proteins. Scope and approach This review focuses on the application of food proteins nanoimaging by AFM and contains two parts. In this part I, the technical information of AFM food protein research is summarized and discussed. Firstly, this review introduces the components and imaging modes of AFM imaging. Secondly, this review summarizes the observation ways of AFM imaging for food proteins. Thirdly, this review discussed the research types of AFM nanoimaging for food protein research according to different research needs. Finally, the advantages and disadvantages of AFM for food protein nanoimaging are summarized. Key findings and conclusions This review part I can provide comprehensive technical information of AFM nanoimaging for food protein research to those who are interested to enter this field. As a powerful nanotech imaging tool, AFM has many advantages for food protein research and will undoubtedly be applied to study a growing number of food proteins in the future. AFM has become an important nanotech tool to analyze proteins and many food scientists have used it to analyze food proteins in the past three decades. This review focuses on the application of AFM nanoimaging and contains two parts. In this part I, the AFM components, imaging modes, observation ways, and research types according to different research needs are reviewed and discussed in this part I. The advantages and disadvantages of AFM for food protein nanoimaging are also discussed. The part I of this review provides comprehensive technical information of AFM nanoimaging for food proteins.