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1.  Cell type-specific delivery of short interfering RNAs by dye-functionalised theranostic nanoparticles 
Nature Communications  2014;5:5565.
Efficient delivery of short interfering RNAs reflects a prerequisite for the development of RNA interference therapeutics. Here, we describe highly specific nanoparticles, based on near infrared fluorescent polymethine dye-derived targeting moieties coupled to biodegradable polymers. The fluorescent dye, even when coupled to a nanoparticle, mimics a ligand for hepatic parenchymal uptake transporters resulting in hepatobiliary clearance of approximately 95% of the dye within 45 min. Body distribution, hepatocyte uptake and excretion into bile of the dye itself, or dye-coupled nanoparticles can be tracked by intravital microscopy or even non-invasively by multispectral optoacoustic tomography. Efficacy of delivery is demonstrated in vivo using 3-hydroxy-3-methyl-glutaryl-CoA reductase siRNA as an active payload resulting in a reduction of plasma cholesterol levels if siRNA was formulated into dye-functionalised nanoparticles. This suggests that organ-selective uptake of a near infrared dye can be efficiently transferred to theranostic nanoparticles allowing novel possibilities for personalised silencing of disease-associated genes.
A potential drug should specifically interact with its intended target in order to limit unwanted side effects. Here, the authors fabricate a biodegradable polymer nanoparticle with a fluorescent hepatic uptake transporter ligand to achieve targeted in vivo siRNA delivery and imaging of delivery.
doi:10.1038/ncomms6565
PMCID: PMC4268698  PMID: 25470305
2.  Raman Imaging with a Fiber-Coupled Multichannel Spectrograph 
Sensors (Basel, Switzerland)  2014;14(11):21968-21980.
Until now, spatially resolved Raman Spectroscopy has required to scan a sample under investigation in a time-consuming step-by-step procedure. Here, we present a technique that allows the capture of an entire Raman image with only one single exposure. The Raman scattering arising from the sample was collected with a fiber-coupled high-performance astronomy spectrograph. The probe head consisting of an array of 20 × 20 multimode fibers was linked to the camera port of a microscope. To demonstrate the high potential of this new concept, Raman images of reference samples were recorded. Entire chemical maps were received without the need for a scanning procedure.
doi:10.3390/s141121968
PMCID: PMC4279572  PMID: 25420149
multichannel Raman spectroscopy; astronomy spectrograph; optical fiber bundle; Raman imaging
3.  Raman Spectroscopy as a Potential Tool for Detection of Brucella spp. in Milk 
Applied and Environmental Microbiology  2012;78(16):5575-5583.
Detection of Brucella, causing brucellosis, is very challenging, since the applied techniques are mostly time-demanding and not standardized. While the common detection system relies on the cultivation of the bacteria, further classical typing up to the biotype level is mostly based on phenotypic or genotypic characteristics. The results of genotyping do not always fit the existing taxonomy, and misidentifications between genetically closely related genera cannot be avoided. This situation gets even worse, when detection from complex matrices, such as milk, is necessary. For these reasons, the availability of a method that allows early and reliable identification of possible Brucella isolates for both clinical and epidemiological reasons would be extremely useful. We evaluated micro-Raman spectroscopy in combination with chemometric analysis to identify Brucella from agar plates and directly from milk: prior to these studies, the samples were inactivated via formaldehyde treatment to ensure a higher working safety. The single-cell Raman spectra of different Brucella, Escherichia, Ochrobactrum, Pseudomonas, and Yersinia spp. were measured to create two independent databases for detection in media and milk. Identification accuracies of 92% for Brucella from medium and 94% for Brucella from milk were obtained while analyzing the single-cell Raman spectra via support vector machine. Even the identification of the other genera yielded sufficient results, with accuracies of >90%. In summary, micro-Raman spectroscopy is a promising alternative for detecting Brucella. The measurements we performed at the single-cell level thus allow fast identification within a few hours without a demanding process for sample preparation.
doi:10.1128/AEM.00637-12
PMCID: PMC3406119  PMID: 22660699
4.  Liver Dysfunction and Phosphatidylinositol-3-Kinase Signalling in Early Sepsis: Experimental Studies in Rodent Models of Peritonitis 
PLoS Medicine  2012;9(11):e1001338.
Experimental studies in a rat model of fecal peritonitis conducted by Michael Bauer and colleagues show that in this model, changes in liver function occur early in the development of sepsis, with potential implications for prognosis and development of new therapeutic approaches.
Background
Hepatic dysfunction and jaundice are traditionally viewed as late features of sepsis and portend poor outcomes. We hypothesized that changes in liver function occur early in the onset of sepsis, yet pass undetected by standard laboratory tests.
Methods and Findings
In a long-term rat model of faecal peritonitis, biotransformation and hepatobiliary transport were impaired, depending on subsequent disease severity, as early as 6 h after peritoneal contamination. Phosphatidylinositol-3-kinase (PI3K) signalling was simultaneously induced at this time point. At 15 h there was hepatocellular accumulation of bilirubin, bile acids, and xenobiotics, with disturbed bile acid conjugation and drug metabolism. Cholestasis was preceded by disruption of the bile acid and organic anion transport machinery at the canalicular pole. Inhibitors of PI3K partially prevented cytokine-induced loss of villi in cultured HepG2 cells. Notably, mice lacking the PI3Kγ gene were protected against cholestasis and impaired bile acid conjugation. This was partially confirmed by an increase in plasma bile acids (e.g., chenodeoxycholic acid [CDCA] and taurodeoxycholic acid [TDCA]) observed in 48 patients on the day severe sepsis was diagnosed; unlike bilirubin (area under the receiver-operating curve: 0.59), these bile acids predicted 28-d mortality with high sensitivity and specificity (area under the receiver-operating curve: CDCA: 0.77; TDCA: 0.72; CDCA+TDCA: 0.87).
Conclusions
Liver dysfunction is an early and commonplace event in the rat model of sepsis studied here; PI3K signalling seems to play a crucial role. All aspects of hepatic biotransformation are affected, with severity relating to subsequent prognosis. Detected changes significantly precede conventional markers and are reflected by early alterations in plasma bile acids. These observations carry important implications for the diagnosis of liver dysfunction and pharmacotherapy in the critically ill. Further clinical work is necessary to extend these concepts into clinical practice.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Sepsis (blood poisoning)—a life-threatening condition caused by an inappropriate immune response to an infection—is a major global cause of death. Normally, when bacteria or other microbes enter the human body, the immune system efficiently destroys the invaders. In sepsis the immune system goes into overdrive, and the chemicals it releases into the blood to combat the infection trigger widespread inflammation (swelling). This leads to the formation of small blood clots and leaky blood vessels that block the flow of blood to vital organs such as the kidneys and liver. In the most severe cases, multiple organs fail and the patient dies. Anyone can get sepsis, but people with weakened immune systems, the very young, and the elderly are most vulnerable. Symptoms of sepsis include fever, chills, rapid breathing, a fast heart rate, and confusion. In its early stages, sepsis can be treated with antibiotics alone, but people with severe sepsis need to be admitted to an intensive care unit where the vital organs can be supported while the infection is treated.
Why Was This Study Done?
Thirty to fifty percent of people who develop severe sepsis die. If sepsis could be diagnosed in its early stages, it might be possible to save more people. Unfortunately, the symptoms of sepsis mimic those of other conditions, and, because sepsis tends to develop very quickly, it is often not diagnosed until it is too late to save the patient's life. The development of liver (hepatic) dysfunction and jaundice are both regarded as late features of sepsis (jaundice is yellowing of the skin and eyes caused by a build-up of bilirubin in the blood). However, the researchers hypothesized that changes in liver function occur early in sepsis and could, therefore, be used to improve the diagnosis and management of sepsis.
What Did the Researchers Do and Find?
The researchers induced sepsis in rats by injecting bacteria into the peritoneal cavity (the gap between the abdominal wall and the abdominal organs), separated the infected animals into predicted survivors and non-survivors based on their heart stroke volume measured using cardiac ultrasound, and then examined their liver function. The expression of genes encoding proteins involved in “biotransformation” and “hepatobiliary transport” (the processes that convert waste products and toxic chemicals into substances that can be conjugated to increase solubility and then excreted) was down-regulated within six hours of sepsis induction in the predicted non-survivors compared to the predicted survivors. Functional changes such as bilirubin and bile acid accumulation in the liver (cholestasis), poor excretion of xenobiotics (molecules not usually found in the body such as antibiotics), and disturbed bile acid conjugation were also seen in predicted non-survivors but not in survivors. Moreover, phosphatidylinositol-3-kinase (PI3K) signaling (which is involved in several immune processes) increased soon after sepsis induction in non-survivor but not in survivor animals. Notably, mice lacking the PI3Kγ gene did not develop cholestasis or show impaired bile acid conjugation after induction of sepsis. Finally, in human patients, plasma bile acids were increased in 48 patients on the day that severe sepsis was diagnosed, and these increases accurately predicted death in these patients.
What Do These Findings Mean?
These findings show that liver dysfunction is an early event in animal models of sepsis and that PI3K signalling plays a crucial role in the development of liver dysfunction. They show that all aspects of liver biotransformation are affected during sepsis and suggest that outcomes are related to the severity of these changes. The limited clinical data included in this study also support the hypothesis that changes in liver function occur early in sepsis, although these data need confirming and extending. Taken together, these findings suggest that liver function tests might aid early diagnosis of sepsis and might also provide information about likely outcomes. They also have important implications for the use of drugs in patients who are critically ill with sepsis, in that some of the drugs routinely administered to such patients may not be adequately detoxified and may, therefore, contribute to organ injury. Finally, these findings suggest that inhibition of PI3Kγ may alleviate sepsis-associated cholestasis.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001338.
This study is further discussed in a PLOS Medicine Perspective by John Marshall
The US National Institute of General Medical Sciences has a fact sheet on sepsis
The UK National Health Service Choices website has information about sepsis and about jaundice
The Surviving Sepsis Campaign, which was developed to improve the management, diagnosis, and treatment of sepsis, provides basic information about sepsis
The Sepsis Alliance, a US not-for-profit organization, also provides information about sepsis for patients and their families, including personal stories about sepsis
The not-for profit UK Sepsis Trust is another useful source of information about sepsis that includes patient stories
MedlinePlus provides links to additional resources about sepsis and jaundice (in English and Spanish)
doi:10.1371/journal.pmed.1001338
PMCID: PMC3496669  PMID: 23152722
5.  Calcite Biomineralization by Bacterial Isolates from the Recently Discovered Pristine Karstic Herrenberg Cave 
Karstic caves represent one of the most important subterranean carbon storages on Earth and provide windows into the subsurface. The recent discovery of the Herrenberg Cave, Germany, gave us the opportunity to investigate the diversity and potential role of bacteria in carbonate mineral formation. Calcite was the only mineral observed by Raman spectroscopy to precipitate as stalactites from seepage water. Bacterial cells were found on the surface and interior of stalactites by confocal laser scanning microscopy. Proteobacteria dominated the microbial communities inhabiting stalactites, representing more than 70% of total 16S rRNA gene clones. Proteobacteria formed 22 to 34% of the detected communities in fluvial sediments, and a large fraction of these bacteria were also metabolically active. A total of 9 isolates, belonging to the genera Arthrobacter, Flavobacterium, Pseudomonas, Rhodococcus, Serratia, and Stenotrophomonas, grew on alkaline carbonate-precipitating medium. Two cultures with the most intense precipitate formation, Arthrobacter sulfonivorans and Rhodococcus globerulus, grew as aggregates, produced extracellular polymeric substances (EPS), and formed mixtures of calcite, vaterite, and monohydrocalcite. R. globerulus formed idiomorphous crystals with rhombohedral morphology, whereas A. sulfonivorans formed xenomorphous globular crystals, evidence for taxon-specific crystal morphologies. The results of this study highlighted the importance of combining various techniques in order to understand the geomicrobiology of karstic caves, but further studies are needed to determine whether the mineralogical biosignatures found in nutrient-rich media can also be found in oligotrophic caves.
doi:10.1128/AEM.06568-11
PMCID: PMC3273019  PMID: 22179248
6.  The morphology of silver nanoparticles prepared by enzyme-induced reduction 
Summary
Silver nanoparticles were synthesized by an enzyme-induced growth process on solid substrates. In order to customize the enzymatically grown nanoparticles (EGNP) for analytical applications in biomolecular research, a detailed study was carried out concerning the time evolution of the formation of the silver nanoparticles, their morphology, and their chemical composition. Therefore, silver-nanoparticle films of different densities were investigated by using scanning as well as transmission electron microscopy to examine their structure. Cross sections of silver nanoparticles, prepared for analysis by transmission electron microscopy were additionally studied by energy-dispersive X-ray spectroscopy in order to probe their chemical composition. The surface coverage of substrates with silver nanoparticles and the maximum particle height were determined by Rutherford backscattering spectroscopy. Variations in the silver-nanoparticle films depending on the conditions during synthesis were observed. After an initial growth state the silver nanoparticles exhibit the so-called desert-rose or nanoflower-like structure. This complex nanoparticle structure is in clear contrast to the auto-catalytically grown spherical particles, which maintain their overall geometrical appearance while increasing their diameter. It is shown, that the desert-rose-like silver nanoparticles consist of single-crystalline plates of pure silver. The surface-enhanced Raman spectroscopic (SERS) activity of the EGNP structures is promising due to the exceptionally rough surface structure of the silver nanoparticles. SERS measurements of the vitamin riboflavin incubated on the silver nanoparticles are shown as an exemplary application for quantitative analysis.
doi:10.3762/bjnano.3.47
PMCID: PMC3388365  PMID: 23016145
EGNP; enzymatically grown silver nanoparticles; enzyme-induced deposition; nanoflower; SERS
7.  A study of Docetaxel-induced effects in MCF-7 cells by means of Raman microspectroscopy 
Chemotherapies feature a low success rate of about 25%, and therefore, the choice of the most effective cytostatic drug for the individual patient and monitoring the efficiency of an ongoing chemotherapy are important steps towards personalized therapy. Thereby, an objective method able to differentiate between treated and untreated cancer cells would be essential. In this study, we provide molecular insights into Docetaxel-induced effects in MCF-7 cells, as a model system for adenocarcinoma, by means of Raman microspectroscopy combined with powerful chemometric methods. The analysis of the Raman data is divided into two steps. In the first part, the morphology of cell organelles, e.g. the cell nucleus has been visualized by analysing the Raman spectra with k-means cluster analysis and artificial neural networks and compared to the histopathologic gold standard method hematoxylin and eosin staining. This comparison showed that Raman microscopy is capable of displaying the cell morphology; however, this is in contrast to hematoxylin and eosin staining label free and can therefore be applied potentially in vivo. Because Docetaxel is a drug acting within the cell nucleus, Raman spectra originating from the cell nucleus region were further investigated in a next step. Thereby we were able to differentiate treated from untreated MCF-7 cells and to quantify the cell–drug response by utilizing linear discriminant analysis models.
FigureRaman microspectroscopy in combination with powerful chemometric methods (e.g. artificial neural networks) indicates morphological (nucleus fragmentation) and spectral changes in Docetaxel treated breast cancer cells (MCF-7) in comparison to untreated cell samples
Electronic supplementary material
The online version of this article (doi:10.1007/s00216-012-5887-9) contains supplementary material, which is available to authorized users.
doi:10.1007/s00216-012-5887-9
PMCID: PMC3336052  PMID: 22399121
Raman microspectroscopy; Docetaxel; Breast cancer; MCF-7; Chemistry; Biochemistry, general; Characterization and Evaluation of Materials; Analytical Chemistry; Environmental Monitoring/Analysis; Food Science; Laboratory Medicine
8.  Towards multiple readout application of plasmonic arrays 
Summary
In order to combine the advantages of fluorescence and surface-enhanced Raman spectroscopy (SERS) on the same chip platform, a nanostructured gold surface with a unique design, allowing both the sensitive detection of fluorescence light together with the specific Raman fingerprint of the fluorescent molecules, was established. This task requires the fabrication of plasmonic arrays that permit the binding of molecules of interest at different distances from the metallic surface. The most efficient SERS enhancement is achieved for molecules directly adsorbed on the metallic surface due to the strong field enhancement, but where, however, the fluorescence is quenched most efficiently. Furthermore, the fluorescence can be enhanced efficiently by careful adjustment of the optical behavior of the plasmonic arrays. In this article, the simultaneous application of SERS and fluorescence, through the use of various gold nanostructured arrays, is demonstrated by the realization of a DNA detection scheme. The results shown open the way to more flexible use of plasmonic arrays in bioanalytics.
doi:10.3762/bjnano.2.54
PMCID: PMC3190620  PMID: 22003456
fluorescence; multiple readout; plasmonic array; surface-enhanced fluorescence (SEF); surface-enhanced Raman spectroscopy (SERS)
9.  Charge Isomers of Myelin Basic Protein: Structure and Interactions with Membranes, Nucleotide Analogues, and Calmodulin 
PLoS ONE  2011;6(5):e19915.
As an essential structural protein required for tight compaction of the central nervous system myelin sheath, myelin basic protein (MBP) is one of the candidate autoantigens of the human inflammatory demyelinating disease multiple sclerosis, which is characterized by the active degradation of the myelin sheath. In this work, recombinant murine analogues of the natural C1 and C8 charge components (rmC1 and rmC8), two isoforms of the classic 18.5-kDa MBP, were used as model proteins to get insights into the structure and function of the charge isomers. Various biochemical and biophysical methods such as size exclusion chromatography, calorimetry, surface plasmon resonance, small angle X-ray and neutron scattering, Raman and fluorescence spectroscopy, and conventional as well as synchrotron radiation circular dichroism were used to investigate differences between these two isoforms, both from the structural point of view, and regarding interactions with ligands, including calmodulin (CaM), various detergents, nucleotide analogues, and lipids. Overall, our results provide further proof that rmC8 is deficient both in structure and especially in function, when compared to rmC1. While the CaM binding properties of the two forms are very similar, their interactions with membrane mimics are different. CaM can be used to remove MBP from immobilized lipid monolayers made of synthetic lipids - a phenomenon, which may be of relevance for MBP function and its regulation. Furthermore, using fluorescently labelled nucleotides, we observed binding of ATP and GTP, but not AMP, by MBP; the binding of nucleoside triphosphates was inhibited by the presence of CaM. Together, our results provide important further data on the interactions between MBP and its ligands, and on the differences in the structure and function between MBP charge isomers.
doi:10.1371/journal.pone.0019915
PMCID: PMC3102069  PMID: 21647440
10.  Chemotaxonomic Identification of Single Bacteria by Micro-Raman Spectroscopy: Application to Clean-Room-Relevant Biological Contaminations 
Microorganisms, such as bacteria, which might be present as contamination inside an industrial food or pharmaceutical clean room process need to be identified on short time scales in order to minimize possible health hazards as well as production downtimes causing financial deficits. Here we describe the first results of single-particle micro-Raman measurements in combination with a classification method, the so-called support vector machine technique, allowing for a fast, reliable, and nondestructive online identification method for single bacteria.
doi:10.1128/AEM.71.3.1626-1637.2005
PMCID: PMC1065155  PMID: 15746368
11.  Evaluation of Colloids and Activation Agents for Determination of Melamine Using UV-SERS 
UV-SERS measurements offer a great potential for environmental or food (detection of food contaminats) analytics. Here, the UV-SERS enhancement potential of various kinds of metal colloids, such as Pd, Pt, Au, Ag, Au–Ag core–shell, and Ag–Au core–shell with different shapes and sizes, were studied using melamine as a test molecule. The influence of different activation (KF, KCl, KBr, K2SO4) agents onto the SERS activity of the nanomaterials was investigated, showing that the combination of a particular nanoparticle with a special activation agent is extremely crucial for the observed SERS enhancement. In particular, the size dependence of spherical nanoparticles of one particular metal on the activator has been exploited. By doing so, it could be shown that the SERS enhancement increases or decreases for increasing or decreasing size of a nanoparticle, respectively. Overall, the presented results demonstrate the necessity to adjust the nanoparticle size and the activation agent for different experiments in order to achieve the best possible UV-SERS results.
doi:10.1021/jp211863y
PMCID: PMC3304507  PMID: 22428076

Results 1-11 (11)