Raman spectroscopic analysis of the molecular composition of oral cavity squamous cell carcinoma and healthy tongue tissue.

A Raman tissue spectrum is a quantitative representation of the overall molecular composition of that tissue. Raman spectra are often used as tissue fingerprints without further interpretation of the specific information that they contain about the tissue's molecular composition. In this study, we analyzed the differences in molecular composition between oral cavity squamous cell carcinoma (OCSCC) and healthy tissue structures in tongue, based on their Raman spectra. A total of 1087 histopathologically annotated spectra (142 OCSCC, 202 surface squamous epithelium, 61 muscle, 65 adipose tissue, 581 connective tissue, 26 gland, and 10 nerve) were obtained from Raman maps of 44 tongue samples from 21 patients. A characteristic, average spectrum of each tissue structure was fitted with a set of 55 pure-compound reference spectra, to define the best library of fit-spectra. Reference spectra represented proteins, lipids, nucleic acids, carbohydrates, amino acids and other miscellaneous molecules. A non-negative least-squares algorithm was used for fitting. Individual spectra per histopathological annotation were then fitted with this selected library in order to determine the molecular composition per tissue structure. The spectral contribution per chemical class was calculated. The results show that all characteristic tissue-type spectra could be fitted with a low residual of <4.82%. The content of carbohydrates, proteins and amino acids was the strongest discriminator between OCSCC and healthy tissue. The combination of carbohydrates, proteins and amino acids was used for a classification model of 'tumor' versus 'healthy tissue'. Validation of this model on an independent dataset showed a specificity of 93% at a sensitivity of 100%.

Determination of natural moisturizing factors in the skin: Raman microspectroscopy versus HPLC.

BACKGROUND: Natural moisturizing factor (NMF) is used as genotypic and phenotypic biomarker in diagnostics. This study is a side-to-side comparison of two different methods to determine NMF in atopic dermatitis patients: Raman microspectroscopy and stratum corneum tape stripping followed by HPLC. RESULTS: Measured NMF values were significantly correlated (R2 = .61; p < .0001), both methods demonstrated a concentration-depth dependence of NMF and reduced NMF levels in the carriers of filaggrin null mutations. Good agreement between measurements of left and right arms indicated robustness and good reproducibility of both methods. CONCLUSIONS: Both methods showed comparable performance, choice of method will rather be influenced by practical consideration.

Lipid to protein ratio plays an important role in the skin barrier function in patients with atopic eczema.

BACKGROUND: The barrier function of the skin is primarily provided by the stratum corneum (SC), the outermost layer of the skin. Skin barrier impairment is thought to be a primary factor in the pathogenesis of atopic eczema (AE). Filaggrin is an epidermal barrier protein and common mutations in the filaggrin gene strongly predispose for AE. However, the role of filaggrin mutations in the decreased skin barrier in AE is not fully understood. It was recently shown that changes in SC lipid composition and organization play a role in the reduced skin barrier in AE. OBJECTIVES: To determine whether the lipid/protein ratio and the total dry SC mass per surface area are related to the skin barrier function of controls and patients with AE. METHODS: A case-control study was performed to compare nonlesional and lesional skin of AE with skin of controls. The dry SC mass was determined by tape-stripping and Squamescan(™) . The ratio between lipid and protein bands in the Raman spectrum was used to determine the lipid/protein ratio. Skin barrier function was assessed by transepidermal water loss. RESULTS: The results show that the dry SC mass per skin area is altered only in lesional SC of patients with AE compared with control subjects. The observed reduction in the lipid/protein ratio in SC of patients with AE was more pronounced, both in lesional and nonlesional SC and correlated strongly with the skin barrier function and disease severity. CONCLUSIONS: The lipid/protein ratio plays a role in the reduced skin barrier function in AE.

Raman spectroscopy with an integrated arrayed-waveguide grating.

An integrated arrayed-waveguide grating fabricated in silicon-oxynitride technology is applied to Raman spectroscopy. After its validation by reproducing the well-known spectrum of cyclohexane, polarized Raman spectra are measured of extracted human teeth containing localized initial carious lesions. Excellent agreement is obtained between the spectra of healthy and carious tooth enamel measured with our integrated device and spectra recorded using a conventional Raman spectrometer. Our results represent a step toward the realization of compact, hand-held, integrated spectrometers, e.g. for the detection of dental caries at an early stage.

Experimental study on needle insertion force to minimize tissue deformation in tongue tissue.

This study reports on the effects of insertion velocity, needle tip geometry and needle diameter on tissue deformation and maximum insertion force. Moreover, the effect of multiple insertions with the same needle on the maximum insertion force is reported. The tissue deformation and maximum insertion force strongly depend on the insertion velocity and the tip geometry. No correlation was found between the outer diameter and the maximum insertion force for small needles (30G - 32G). The endurance experiments showed no remarkable difference in the maximum insertion force during 100 insertions.

Conserved repetitive epitope recognized by CD4+ clones from a malaria-immunized volunteer.

T cell clones obtained from a human volunteer immunized with Plasmodium falciparum sporozoites specifically recognized the native circumsporozoite (CS) antigen expressed on P. falciparum sporozoites, as well as bacteria- and yeast-derived recombinant falciparum CS proteins. The response of these CD4+ CD8- cells was species-specific, since the clones did not proliferate or secrete gamma interferon when challenged with sporozoites or recombinant CS proteins of other human, simian, or rodent malarias. The epitope recognized by the sporozoite-specific human T cell clones mapped to the 5' repeat region of the CS protein and was contained in the NANPNVDPNANP sequence.

Cyclophilin-promoted folding of mouse dihydrofolate reductase does not include the slow conversion of the late-folding intermediate to the active enzyme.

Cyclophilins accelerate slow protein folding reactions in vitro by catalyzing the cis/trans isomerization of peptidyl-prolyl bonds. Cyclophilins were reported to be involved in a variety of cellular functions, including the promotion of protein folding by use of the substrate mouse dihydrofolate reductase (DHFR). The interaction of cyclophilin with DHFR has only been studied under limited conditions so far, not taking into account that native DHFR exists in equilibrium with a non-native late-folding intermediate. Here we report a systematic analysis of catalysis of DHFR folding by cyclophilins. The specific ligand methotrexate traps DHFR in its native state, permitting a specific analysis of the action of cyclophilin on both denatured DHFR with non-native prolyl bonds and denatured DHFR with all-native prolyl bonds. Cyclophilins from yeast and Neurospora crassa as well as the related prolyl isomerase b from Escherichia coli promote the folding of different forms of DHFR to the enzymatically active form, demonstrating the generality of cyclophilin-catalyzed folding of DHFR. The slow equilibrium between the late-folding intermediate and native DHFR suggests that prolyl isomerization may be required for this final phase of conversion to native DHFR. However, by reversible trapping of the intermediate, we analyze the slow interconversion between native and late-folding conformations in the backward and forward reactions and show a complete independence of cyclophilin. We conclude that cyclophilin catalyzes folding of DHFR, but surprisingly not in the last slow folding step.

Tissue characterization using high wave number Raman spectroscopy.

Raman spectroscopy is a powerful diagnostic tool, enabling tissue identification and classification. Mostly, the so-called fingerprint (approximately 400-1800 cm(-1)) spectral region is used. In vivo application often requires small flexible fiber-optic probes, and is hindered by the intense Raman signal that is generated in the fused silica core of the fiber. This necessitates filtering of laser light, which is guided to the tissue, and of the scattered light collected from the tissue, leading to complex and expensive designs. Fused silica has no Raman signal in the high wave number region (2400-3800 cm(-1)). This enables the use of a single unfiltered fiber to guide laser light to the tissue and to collect scattered light in this spectral region. We show, by means of a comparison of in vitro Raman microspectroscopic maps of thin tissue sections (brain tumors, bladder), measured both in the high wave number region and in the fingerprint region, that essentially the same diagnostic information is obtained in the two wave number regions. This suggests that for many clinical applications the technological hurdle of designing and constructing suitable fiber-optic probes may be eliminated by using the high wave number region and a simple piece of standard optical fiber.

In vivo confocal Raman microspectroscopy of the skin: noninvasive determination of molecular concentration profiles.

Confocal Raman spectroscopy is introduced as a noninvasive in vivo optical method to measure molecular concentration profiles in the skin. It is shown how it can be applied to determine the water concentration in the stratum corneum as a function of distance to the skin surface, with a depth resolution of 5 microm. The resulting in vivo concentration profiles are in qualitative and quantitative agreement with published data, obtained by in vitro X-ray microanalysis of skin samples. Semi-quantitative concentration profiles were determined for the major constituents of natural moisturizing factor (serine, glycine, pyrrolidone-5-carboxylic acid, arginine, ornithine, citrulline, alanine, histidine, urocanic acid) and for the sweat constituents lactate and urea. A detailed description is given of the signal analysis methodology that enables the extraction of this information from the skin Raman spectra. No other noninvasive in vivo method exists that enables an analysis of skin molecular composition as a function of distance to the skin surface with similar detail and spatial resolution. Therefore, it may be expected that in vivo confocal Raman spectroscopy will find many applications in basic and applied dermatologic research.

Domain organization and molecular characterization of 13 two-component systems identified by genome sequencing of Streptococcus pneumoniae.

In bacteria, adaptive responses to environmental stimuli are often initiated by two-component signal transduction systems (TCS). The prototypical TCS comprises two proteins: a histidine kinase (HK, hk) and a response regulator (RR rr). Recent research has suggested that compounds that inhibit two-component systems might have good antibacterial activity. In order to identify TCS that are crucial for growth or virulence of Streptococcus pneumoniae, we have examined the genomic sequence of a virulent S. pneumoniae strain for genes that are related to known histidine kinases or response regulators. Altogether 13 histidine kinases and 13 response regulators have been identified. The protein sequences encoded by these genes were compared with sequences deposited in public databases. This analysis revealed that two of the 13 pneumococcal TCSs have been described before (ciaRH and comDE) and two are homologous to the yycFG and the phoRP genes of Bacillus subtilis. All the pneumococcal response regulators contain putative DNA binding motifs within the C-terminal output domain, implying that they are involved in transcriptional control. Two of these response regulators are obviously the first representatives of a new subfamily containing an AraC-type DNA-binding effector domain. To assess the regulatory role of these transcription factors, we disrupted each of the 13 response regulator genes by insertional mutagenesis. All the viable mutant strains with disrupted response regulator genes were further characterized with regard to growth in vitro, competence, and experimental virulence. Two response regulator genes could not be inactivated, indicating that they may regulate essential cellular functions. The possibility of using these systems as targets for the development of novel antibacterials will be discussed.

A Plasmodium falciparum malaria vaccine candidate which contains epitopes from the circumsporozoite protein and a blood stage antigen, 5.1.

The previously described Plasmodium falciparum blood stage antigen, 5.1 (also referred to as exp-1) was expressed at a high level in Escherichia coli. Saimiri monkeys immunised with purified recombinant antigen 5.1 were partially protected from P. falciparum blood stage parasite challenge. The gene coding for 5.1 was combined with DNA coding for an (Asn-Ala-Asn-Pro)19 sequence (abbreviated (NANP)19 in the one-letter amino acid code). To facilitate purification of the recombinant protein, DNA coding for a hexahistidine (His6) sequence was introduced at the 5' end of the gene (proteins containing His6 have high affinity for Ni(2+)-chelate columns even in the presence of 6 M guanidine HCl). The recombinant protein, His6-5.1-(NANP)19 with an apparent molecular size of 40 kDa could be highly purified by a combination of 4 steps: (1) release and solubilization of the recombinant fusion protein from E. coli in the presence of 6 M guanidine-HCl; (2) precipitation of over 60% of the bacterial proteins by the addition of ammonium sulphate to 50% saturation; (3) affinity chromatography on a Ni(2+)-chelate column in the presence of 6 M guanidine-HCl; (4) adsorption onto a cation exchange resin in the presence of 6 M urea, and elution with an increasing NaCl gradient. Compared with the previously tested tetanus toxoid-(NANP)3 malaria vaccine, this protein elicits an anti-(NANP)n response which more closely resembles that evoked by native sporozoites. The recombinant vaccine also induces the production of antibodies against the blood stages of the malaria parasite.

Restriction site-free insertion of PCR products directionally into vectors.

A restriction site-free cloning method has been developed for inserting a PCR product into a vector flexibly and precisely at any desired location with high efficiency. The method uses a pair of DNA integration primers with two portions. The 3' portion isolates the inserts by PCR, and the 5' portion integrates the PCR products into the homologous region of the vector. For mutagenesis, a third portion of mutation-generating sequences can be placed in between the 3' and 5' portions. This method has been used to clone the E. coli gene that codes for peptidyl-tRNA hydrolase, expressing it as a native protein and as a glutathione S-transferase fusion protein. It was also applied to convert a construct of the E. coli fatty acid biosynthesis protein with an N-terminal hexa-histidine tag into a construct with a C-terminal hexa-histidine tag.

Recombinant polypeptides for serology of malaria.

We have evaluated 3 molecularly defined polypeptides encoded by encloned Plasmodium falciparum genes for their ability to serve as antigens for detecting antimalaria antibodies. The recombinant proteins correspond to (i) a conserved part of 190-200 kDa schizont merozoite surface component, (ii) the carboxy terminal part of the P. falciparum aldolase, and (iii) the 5.1 antigen. Antibodies were detected using enzyme-linked immunosorbent assays (ELISA) in a high percentage of sera from individuals from a malaria endemic area in The Gambia (up to 99% for some adult groups). These results were further improved, especially for detection of antimalaria antibodies in children, when a pool of all 3 polypeptides (ELISA MIXT) was used as antigen. This ELISA MIXT improves presently available assays for the detection of antimalaria antibodies directed against asexual blood stages in respect of standardization, sensitivity and specificity.

Choice and validation of a near infrared spectroscopic application for the identity control of starting materials. practical experience with the EU draft Note for Guidance on the use of near infrared spectroscopy by the pharmaceutical industry and the data to be forwarded in part II of the dossier for a marketing authorization.

Recently the CPMP/CVMP sent out for consultation the draft Note for Guidance (dNfG) on the use of near infrared spectroscopy (NIRS) by the pharmaceutical industry and the data to be forwarded in part II of the dossier for a marketing authorization. We explored the practicability of this dNfG with respect to the verification of the correct identity of starting materials in a generic tablet-manufacturing site. Within the boundaries of the dNfG, a release procedure was developed for 12 substances containing structurally related compounds and substances differing only in particle size. For the method development literature data were also taken into consideration. Good results were obtained with wavelength correlation (WC), applied on raw spectra or second derivative spectra both without smoothing. The defined threshold of 0.98 for raw spectra differentiated between all molecular structures. Both methods were found to be robust over a period of 1 year. For the differentiation between the different particle sizes a subsequent second chemometric technique had to be used. Soft independent modelling of class analogy (SIMCA) with a probability level of 0.01 proved suitable. Internal and external validation I according to the dNfG showed no incorrect rejections or false acceptances. External validation II according to the dNfG was carried out with 95 potentially interfering substances from which 46 were tested experimentally. Macrogol 400 was not distinguished from macrogol 300. For the complete verification of the identity of macrogol 300 test A of the European Pharmacopoeia is needed in addition to the NIRS application. A release procedure developed with WC applied on raw spectra and SIMCA as a second method, which is different from the preferred method of the dNfG, was tested in practice with good results. We conclude that the dNfG has good practicability and that deviations from the preferred methods of the dNfG can also give good differentiation.

A fast, digitally controlled flow proportional gas injection system for studies in lung function.

The aim of this paper is to describe a device for flow proportional injection of tracer gas in the lungs of mechanically ventilated patients. This device may then be used for the study of the multiple breath indicator gas washout technique to determine the end-expiratory lung volume. Such a tracer gas injection device may also be used in the study of other techniques that rely on uptake and elimination of tracer gas by the lungs. In this paper, an injector is described which enables injection of indicator gas at a predetermined concentration in a breathing circuit independent of the type of breathing. The presented setup uses a control computer to produce steering signals to a multivalve array in proportion to the input breathing signals. The multivalve array consists of ten circular valves, each with a different diameter, which can be opened or closed individually according to the input signal of the array. By opening of a certain combination of valves an amount of sulphur hexafluoride gas proportional to the inspiratory breathing signal is released. The rate of transmission between the components of the injection system was 80 Hz. The injector has a full flow range between 0-10 L/min. The delay time between the breathing signal and the flow response was 70 ms. The aimed washin gas concentration of 1% SF6 was achieved after 0.5 s. The study describes the results of tests to determine valve-flow ratios, step response and dynamic response of the injector. The flow output response of the injector system was shown to increase in input frequencies above 3 Hz. The valve flow ratios showed the largest relative deviation in the two smallest valves of the 10 valve array, respectively 0.005 L/min (25%) and 0.002 L/min (20%). We conclude that the injector can achieve a stable concentration of indicator gas in a breathing system with an accuracy of 0.005 L/min to execute the multiple breath indicator washout test in human subjects. The results of the study indicate that the injector may be of use in other application fields in respiratory physiology in which breathing circuit injection of indicator gas is required.

Overproduction of bacterial chaperones improves the solubility of recombinant protein tyrosine kinases in Escherichia coli.

The production and purification of recombinant proteins from E. coli expression systems is often complicated by the fact that a significant amount of the foreign protein is deposited in the cytoplasm of the bacteria as aggregates or inclusion bodies. Many non-receptor protein tyrosine kinases are typical examples of proteins that are poorly soluble when overproduced in E. coli. Here, we report on the engineering of bacterial strains which overproduce chaperone proteins of the Hsp70 (DnaK, DnaJ and GrpE) and Hsp60 (GroEL and GroES) families. The simultaneous overproduction in E. coli of the chaperones DnaK, DnaJ and GrpE on the one hand, or GroEL and GroES on the other hand, and the human non-receptor protein tyrosine kinases Csk, Fyn or Lck resulted in increased solubility of the recombinant kinases. This provides the basis for future successful production and purification of large quantities of soluble and active non-receptor protein tyrosine kinases from E.coli expression systems and will enable the further characterization of these important enzyme families at the molecular level.

Nucleotide sequence of the prokaryotic mobile genetic element IS30.

The complete nucleotide sequence of the mobile genetic element IS30, a resident of Escherichia coli K12, is 1221 bp long. A large open reading frame, preceded by possible transcription and translation control signals, could encode a basic protein of 383 amino acids which might presumably function as transposase. No large in-frame open reading frame is present on the opposite strand. The 26 bp long terminal inverted repeats have some sequence homology with the c-end of the phage Mu genome and with the terminal inverted repeats of the Halobacterium halobium insertion element ISH50. The IS30 sequence has no significant homology with any other sequenced prokaryotic insertion sequences.

Combined in vivo confocal Raman spectroscopy and confocal microscopy of human skin.

In vivo confocal Raman spectroscopy is a noninvasive optical method to obtain detailed information about the molecular composition of the skin with high spatial resolution. In vivo confocal scanning laser microscopy is an imaging modality that provides optical sections of the skin without physically dissecting the tissue. A combination of both techniques in a single instrument is described. This combination allows the skin morphology to be visualized and (subsurface) structures in the skin to be targeted for Raman measurements. Novel results are presented that show detailed in vivo concentration profiles of water and of natural moisturizing factor for the stratum corneum that are directly related to the skin architecture by in vivo cross-sectional images of the skin. Targeting of skin structures is demonstrated by recording in vivo Raman spectra of sweat ducts and sebaceous glands in situ. In vivo measurements on dermal capillaries yielded high-quality Raman spectra of blood in a completely noninvasive manner. From the results of this exploratory study we conclude that the technique presented has great potential for fundamental skin research, pharmacology (percutaneous transport), clinical dermatology, and cosmetic research, as well as for noninvasive analysis of blood analytes, including glucose.

Effects of temperature and single-stranded DNA on the interaction of an RNA polymerase III transcription factor with a tRNA gene.

It has previously been shown that a yeast RNA polymerase III transcription factor binds stably to tRNA genes. The principal protein-DNA contacts have now been mapped, by dimethylsulfate footprinting, to the vicinity of the A and B block promoter regions of the S. cerevisiae tRNALeu3 gene. Single-stranded DNA preferentially interferes with the binding of the transcription factor to one of the promoter regions. The effect of temperature on the formation of the transcription factor-DNA complex has been examined: the complex has the kind of "opening" property that has been previously associated with prokaryotic RNA polymerase-promoter complexes, with stability increasing as the temperature is raised.