Bioanalytical application of surface‐ and tip‐enhanced Raman spectroscopy

Due to its fingerprint specificity and trace‐level sensitivity, surface‐enhanced Raman spectroscopy (SERS) is an attractive tool in bioanalytics. This review reflects the research in this highly interesting topic of the last 3–4 years. The detection of the SERS signature of biomolecules up to microorganisms and cells is introduced. Labeling using modified nanoparticles (SERS tags) is also introduced. In order to establish biomedical applications, SERS analysis is performed in complex matrices such as body fluids. Furthermore, the SERS technique is combined with other methods such as microfluidic devices for online monitoring and scanning probe microscopy (i.e. tip‐enhanced Raman spectroscopy, TERS) to investigate nanoscaled features. The present review illustrates the broad application fields of SERS and TERS in bioanalytics and shows the great potential of these methods for biomedical diagnostics.     

Advances in TERS (tip-enhanced Raman scattering) for biochemical applications

TERS (tip-enhanced Raman scattering) provides exceptional spatial resolution without any need for labelling and has become a versatile tool for biochemical analysis. Two examples will be highlighted here. On the one hand, TERS measurements on a single mitochondrion are discussed, monitoring the oxidation state of the central iron ion of cytochrome c, leading towards a single protein characterization scheme in a natural environment. On the other hand, a novel approach of single molecule analysis is discussed, again based on TERS experiments on DNA and RNA, further highlighting the resolution capabilities of this method.     

Nanoscale distinction of membrane patches – a TERS study of Halobacterium salinarum

The structural organization of cellular membranes has an essential influence on their functionality. The membrane surfaces currently are considered to consist of various distinct patches, which play an important role in many processes, however, not all parameters such as size and distribution are fully determined. In this study, purple membrane (PM) patches isolated from Halobacterium salinarum were investigated in a first step using TERS (tip‐enhanced Raman spectroscopy). The characteristic Raman modes of the resonantly enhanced component of the purple membrane lattice, the retinal moiety of bacteriorhodopsin, were found to be suitable as PM markers. In a subsequent experiment a single Halobacterium salinarum was investigated with TERS. By means of the PM marker bands it was feasible to identify and localize PM patches on the bacterial surface. The size of these areas was determined to be a few hundred nanometers. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Cover Picture: J. Biophotonics 3/2012

Tip‐enhanced Raman scattering (TERS) on amyloid fibrils – from concept to the actual experiment. A lateral resolution of two nanometers, enough to distinguish distinct amino acids on a protein, is demonstrated. Using the vibrational fingerprint of the molecules no further labeling is required and a direct identification of the primary protein structure is in reach. (Picture: T. Deckert‐Gaudig et al., pp. 215–219 in this issue)     

Towards correlative super‐resolution fluorescence and electron cryo‐microscopy

Correlative light and electron microscopy (CLEM) has become a powerful tool in life sciences. Particularly cryo‐CLEM, the combination of fluorescence cryo‐microscopy (cryo‐FM) permitting for non‐invasive specific multi‐colour labelling, with electron cryo‐microscopy (cryo‐EM) providing the undisturbed structural context at a resolution down to the Ångstrom range, has enabled a broad range of new biological applications. Imaging rare structures or events in crowded environments, such as inside a cell, requires specific fluorescence‐based information for guiding cryo‐EM data acquisition and/or to verify the identity of the structure of interest. Furthermore, cryo‐CLEM can provide information about the arrangement of specific proteins in the wider structural context of their native nano‐environment. However, a major obstacle of cryo‐CLEM currently hindering many biological applications is the large resolution gap between cryo‐FM (typically in the range of ～400 nm) and cryo‐EM (single nanometre to the Ångstrom range). Very recently, first proof of concept experiments demonstrated the feasibility of super‐resolution cryo‐FM imaging and the correlation with cryo‐EM. This opened the door towards super‐resolution cryo‐CLEM, and thus towards direct correlation of structural details from both imaging modalities.     

Comparison and Evaluation of Silver Probe Preparation Techniques for Tip-Enhanced Raman Spectroscopy

In this work, the different procedures for the fabrication of Ag probes for tip-enhanced Raman spectroscopy (TERS) in a top illumination/detection setup are proposed and tested. We focus on technologically simple methods allowing Si tips coated with plasmonic silver nanostructures and bulk metal Ag tips with good shape reproducibility to be produced for atomic force microscopy (AFM) feedback setup. The preparation of Ag TERS probes was based on chemical deposition and vacuum sputtering of Ag on the tips of commercially available Si cantilevers. A straightforward technique for the fabrication of bulk metal Ag probes by the electrochemical etching of Ag microwires was also proposed. Chemically coated, sputtered, and electrochemically etched TERS tips were characterized by scanning electron microscopy (SEM). The produced tips were tested for TERS measurements using graphene oxide (GO) as the target analyte in a top illumination setup. A comparative analysis of enhancement factors (EF) for the different types of tips (probes) is presented in this work.     

Estimation of interaction between oriented immobilized green fluorescent protein and its antibody by high performance affinity chromatography and molecular docking

Although green fluorescence protein (GFP) and its antibody are widely used to track a protein or a cell in life sciences, the binding behavior between them remains unclear. In this work, diazo coupling method that synthesized a new stationary GFP was oriented immobilized on the surface of macro‐porous silica gel by a phase. The stationary phase was utilized to confirm the validation of injection amount‐dependent analysis in exploring protein–protein interaction that use GFP antibody as a probe. GFP antibody was proved to have one type of binding site on immobilized GFP. The number of binding site and association constant were calculated to be (6.41 ± 0.76) × 10^‐10 M and (1.39 ± 0.12) × 10⁹ M^‐1. Further analysis by molecular docking showed that the binding of GFP to its antibody is mainly driven by hydrogen bonds and salt bridges. These results indicated that injection amount‐dependent analysis is capable of exploring the protein–protein interactions with the advantages of ligand and time saving. It is a valuable methodology for the ligands, which are expensive or difficult to obtain. Copyright © 2015 John Wiley & Sons, Ltd.     

Investigation of Tip-Enhanced Raman Spectroscopy on a Silver Nanohole Array Substrate

Plasmonics - Tip-enhanced Raman spectroscopy (TERS) has received much attention due to excellent spatial resolution and high detection sensitivity. However, its performance depends crucially on the...     

1,3,5‐Trihydroxy‐13,13‐dimethyl‐2H‐pyran [7,6‐b] xanthone directly targets heat shock protein 27 in hepatocellular carcinoma

We previously showed that the small molecule 1,3,5‐trihydroxy‐13,13‐dimethyl‐2H‐pyran [7,6‐b] xanthone (TDP) induces apoptosis in hepatocellular carcinoma (HCC) by suppressing Hsp27 expression, although the mechanism is not fully understood. To investigate the functional association between TDP and Hsp27 protein in HCC, recombinant Hsp27 protein was incubated with TDP at room temperature, and assayed by mass spectrum (MS) and natural electrophoresis. TDP effectively stimulated Hsp27 to form aggregates ex vitro, leading to suppression of its chaperone activity. The aggregates were degraded by the ubiquitin–proteasome (UPS) pathway. TDP directly interacted with Asp17 and Phe55 in chain C of Hsp27 on the basis of bioinformatic prediction. In conclusion, Hsp27 is a direct target of TDP in its anti‐cancer activity, which provides strong support for a clinical application.

     

The way forward in biochar research: targeting trade‐offs between the potential wins

Biochar application to soil is currently widely advocated for a variety of reasons related to sustainability. Typically, soil amelioration with biochar is presented as a multiple‐‘win’ strategy, although it is also associated with potential risks such as environmental contamination. The most often claimed benefits of biochar (i.e. the ‘wins’) include (i) carbon sequestration; (ii) soil fertility enhancement; (iii) biofuel/bioenergy production; (iv) pollutant immobilization; and (v) waste disposal. However, the vast majority of studies ignore possible trade‐offs between them. For example, there is an obvious trade‐off between maximizing biofuel production and maximizing biochar production. Also, relatively little attention has been paid to mechanisms, as opposed to systems impacts, behind observed biochar effects, often leaving open the question as to whether they reflect truly unique properties of biochar as opposed to being simply the short‐term consequences of a fertilization or liming effect. Here, we provide an outline for the future of soil biochar research. We first identify possible trade‐offs between the potential benefits. Second, to be able to better understand and quantify these trade‐offs, we propose guidelines for robust experimental design and selection of appropriate controls that allow both mechanistic and systems assessment of biochar effects and trade‐offs between the wins. Third, we offer a conceptual framework to guide future experiments and suggest guidelines for the standardized reporting of biochar experiments to allow effective between‐site comparisons to quantify trade‐offs. Such a mechanistic and systems framework is required to allow effective comparisons between experiments, across scales and locations, to guide policy and recommendations concerning biochar application to soil.     

Signaling pathway of a photoactivable Rac1-GTPase in the early stages

In modern life‐ and medical‐sciences major efforts are currently concentrated on creating artificial photoenzymes, consisting of light‐ oxygen‐voltage‐sensitive (LOV) domains fused to a target enzyme. Such protein constructs possess great potential for controlling the cell metabolism as well as gene function upon light stimulus. This has recently been impressively demonstrated by designing a novel artificial fusion protein, connecting the AsLOV2‐Jα‐photosensor from Avena sativa with the Rac1‐GTPase (AsLOV2‐Jα‐Rac1), and by using it, to control the motility of cancer cells from the HeLa‐line. Although tremendous progress has been achieved on the generation of such protein constructs, a detailed understanding of their signaling pathway after photoexcitation is still in its infancy. Here, we show through computer simulations of the AsLOV2‐Jα‐Rac1‐photoenzyme that the early processes after formation of the Cys450‐FMN‐adduct involve the breakage of a H‐bond between the carbonyl oxygen FMN‐C4?O and the amino group of Gln513, followed by a rotational reorientation of its sidechain. This initial event is followed by successive events including β‐sheet tightening and transmission of torsional stress along the Iβ‐sheet, which leads to the disruption of the Jα‐helix from the N‐terminal end. Finally, this process triggers the detachment of the AsLOV2‐Jα‐photosensor from the Rac1‐GTPase, ultimately enabling the activation of Rac1 via binding of the effector protein PAK1. Proteins 2012; © 2012 Wiley Periodicals, Inc.     

High‐throughput cloning and expression library creation for functional proteomics

The study of protein function usually requires the use of a cloned version of the gene for protein expression and functional assays. This strategy is particularly important when the information available regarding function is limited. The functional characterization of the thousands of newly identified proteins revealed by genomics requires faster methods than traditional single‐gene experiments, creating the need for fast, flexible, and reliable cloning systems. These collections of ORF clones can be coupled with high‐throughput proteomics platforms, such as protein microarrays and cell‐based assays, to answer biological questions. In this tutorial, we provide the background for DNA cloning, discuss the major high‐throughput cloning systems (Gateway® Technology, Flexi® Vector Systems, and Creator^TM DNA Cloning System) and compare them side‐by‐side. We also report an example of high‐throughput cloning study and its application in functional proteomics. This tutorial is part of the International Proteomics Tutorial Programme (IPTP12).     

Tracking of nanoscale structural variations on a single amyloid fibril with tip‐enhanced Raman scattering

Amyloid fibrils are known to be responsible for diseases such as Alzheimer's disease. A detailed insight into the structure of amyloid fibrils is fundamental since it is not yet understood what triggers the misfolding of proteins to the fiber like structures. The molecular structure of fibril surfaces on a single amino acid level has not been revealed so far but would present a valuable contribution to this question. Here we demonstrate the direct molecular distinction of selected amino acids on insulin fibril surfaces with a lateral resolution better than 2 nm by applying tip‐enhanced Raman spectroscopy (TERS). This approach provides simultaneously a way to directly reveal conformational changes in the secondary structure, namely α‐helix, β‐sheet, on the fibril surface with nanometer resolution. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

A statistical approach to improve compound screening in cell culture media

The Chinese hamster ovary (CHO) cell line is widely used for the production of recombinant proteins due to its high growing capacity and productivity, as well as other cell lines derived later than CHO. Adapting cell culture media for each specific cell line is a key to exploit these features for cost effective and fast product generation. Media supplementation is generally addressed by means of one‐factor‐at‐a‐time or classical design of experiments approaches but these techniques may not be efficient enough in preliminary screening phases. In this study, a novel strategy consisting in folding over the Plackett–Burman design was used to increase cell growth and trastuzumab production of different CHO cell lines through supplementation with nonanimal recombinant compounds. Synergies between compounds could be detected with a reduced number of experiments by using this methodology in comparison to more conventional fractional factorial designs. In the particular case reported here, the sequential use of this modified Plackett–Burman in combination with a Box‐Behnken design led to a 1.5‐fold increase in cell growth (10 × 10⁶ cells/mL) and a two‐fold in trastuzumab titer (122 mg/L) in suspension batch culture.     

An optimized chemical synthesis of human relaxin‐2

Human gene 2 relaxin (RLX) is a member of the insulin superfamily and is a multi‐functional factor playing a vital role in pregnancy, aging, fibrosis, cardioprotection, vasodilation, inflammation, and angiogenesis. RLX is currently applied in clinical trials to cure among others acute heart failure, fibrosis, and preeclampsia. The synthesis of RLX by chemical methods is difficult because of the insolubility of its B‐chain and the required laborious and low yielding site‐directed combination of its A (RLXA) and B (RLXB) chains. We report here that oxidation of the Met²⁵ residue of RLXB improves its solubility, allowing its effective solid‐phase synthesis and application in random interchain combination reactions with RLXA. Linear Met(O)²⁵‐RLX B‐chain (RLXBO) reacts with a mixture of isomers of bicyclic A‐chain (bcRLXA) giving exclusively the native interchain combination. Applying this method Met(O)²⁵‐RLX (RLXO) was obtained in 62% yield and was easily converted to RLX in 78% yield, by reduction with ammonium iodide. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

On Distance‐Based Permutation Tests for Between‐Group Comparisons

Summary Permutation tests based on distances among multivariate observations have found many applications in the biological sciences. Two major testing frameworks of this kind are multiresponse permutation procedures and pseudo‐F tests arising from a distance‐based extension of multivariate analysis of variance. In this article, we derive conditions under which these two frameworks are equivalent. The methods and equivalence results are illustrated by reanalyzing an ecological data set and by a novel application to functional magnetic resonance imaging data.     

Excitation Dynamics in Low Band Gap Donor–Acceptor Copolymers and Blends

Donor–acceptor (D–A) type copolymers show great potential for the application in the active layer of organic solar cells. Nevertheless the nature of the excited states, the coupling mechanism and the relaxation pathways following photoexcitation are yet to be clarified. We carried out comparative measurements of the steady state absorption and photoluminescence (PL) on the copolymer poly[N‐(1‐octylnonyl)‐2,7‐carbazole]‐alt‐5,5‐[4′,7′‐di(thien‐2‐yl)‐2′,1′,3′‐benzothiadiazole] (PCDTBT), its building blocks as well as on the newly synthesized N‐(1‐octylnonyl)‐2,7‐bis‐[(5‐phenyl)thien‐2‐yl)carbazole (BPT‐carbazole). The high‐energy absorption band (HEB) of PCDTBT was identified with absorption of carbazoles with adjacent thiophene rings while the low‐energy band (LEB) originates instead from the charge transfer (CT) state delocalized over the aforementioned unit with adjacent benzothiadiazole group. Photoexcitation of the HEB is followed by internal relaxation prior the radiative decay to the ground state. Adding PC₇₀BM results in the efficient PL quenching within the first 50 ps after excitation. From the PL excitation experiments no evidence for a direct electron transfer from the HEB of PCDTBT towards the fullerene acceptor was found, therefore the internal relaxation mechanisms within PCDTBT can be assumed to precede. Our findings indicate that effective coupling between copolymer building blocks governs the photovoltaic performance of the blends.     

Micro‐structured Devices for Chemical Sensing of Flavor and Fragrance

The aim of this study was to design, develop and test an integrated micro‐analytical system. Of special interest are micro‐fluidic and micro‐sensor applications in the field of chemical analysis, such as the optical detection of parameter changes, optical recognition of component profiles and technological micro‐reaction applications. For this purpose, a modular system was developed, which enables the realization of various application cases in an uncomplicated manner, and to execute (via serial or parallel combination of components) usually not compatible tasks. Software components were developed to control the measuring procedure as well as to execute the data interpretation up to a chemometrical discriminant analysis. Application is directed to the production and product control in life sciences mainly for food, natural products, cosmetics and pharmaceutics.     

A Comparison of Weighted Tests for a Slope Change in Simple Regression

Testing for a change in the slope of the simple linear regression model has many applications in bio‐sciences, quality control and survival analysis. This paper compares Anderson‐Darling and Erdós‐Darling type test statistics which are based on the least squares change point process of Sen (1980) with the corresponding Kolmogorov‐Smirnov and Crámer‐von Mises type test statistics. We estimated the limiting critical values of these test statistics and conducted Monte Carlo simulation studies to compare their powers.