Cause of Cambrian Explosion - Terrestrial or Cosmic?

We review the salient evidence consistent with or predicted by the Hoyle-Wickramasinghe (H-W) thesis of Cometary (Cosmic) Biology. Much of this physical and biological evidence is multifactorial. One particular focus are the recent studies which date the emergence of the complex retroviruses of vertebrate lines at or just before the Cambrian Explosion of ∼500 Ma. Such viruses are known to be plausibly associated with major evolutionary genomic processes. We believe this coincidence is not fortuitous but is consistent with a key prediction of H-W theory whereby major extinction-diversification evolutionary boundaries coincide with virus-bearing cometary-bolide bombardment events. A second focus is the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus. A third focus concerns the micro-organism fossil evidence contained within meteorites as well as the detection in the upper atmosphere of apparent incoming life-bearing particles from space. In our view the totality of the multifactorial data and critical analyses assembled by Fred Hoyle, Chandra Wickramasinghe and their many colleagues since the 1960s leads to a very plausible conclusion - life may have been seeded here on Earth by life-bearing comets as soon as conditions on Earth allowed it to flourish (about or just before 4.1 Billion years ago); and living organisms such as space-resistant and space-hardy bacteria, viruses, more complex eukaryotic cells, fertilised ova and seeds have been continuously delivered ever since to Earth so being one important driver of further terrestrial evolution which has resulted in considerable genetic diversity and which has led to the emergence of mankind.

Bone health and SATB2-associated syndrome

SATB2-associated syndrome (SAS) is a rare disorder caused by alterations in the special AT-rich sequence-binding protein 2 (SATB2). Skeletal abnormalities such as tibial bowing, osteomalacia, osteopenia or osteoporosis have been reported suggesting a higher frequency of skeletal complications in SAS. The optimal timing, necessity, and methodology for routine assessment of bone health in individuals with SAS, however, remain unclear. We report molecular and phenotypic features of 7 individuals with SAS documented to have low bone mineral density (BMD) ascertained by dual-energy X-ray absorptiometry (DXA), often preceded by tibial bowing. The lowest BMD Z-scores ranged -2.3 to -5.6. In 4 individuals, total alkaline phosphatase levels were elevated (2 with elevated bone fraction) around the time of low BMD documentation. A clinically significant fracture history and a diagnosis of pediatric osteoporosis were present in 4 individuals. Pamidronate treatment in 2 children improved BMD. In conclusion, low BMD, fractures, and tibial bowing are relatively common skeletal complications in individuals with SAS. DXA is a useful tool when evaluating a child with SAS suspected to have low BMD and the results might alter clinical management.

Schiff base complexes of copper and zinc as potential anti-colitic compounds

The design, synthesis and activity of polymodal compounds for the treatment of inflammatory bowel disease are reported. The compounds, being based on a metal-Schiff base motif, are designed to degrade during intestinal transit to release the bioactive components in the gut. The compounds have been developed sequential with the biomodal compounds combining copper or zinc with a salicylaldehyde adduct. These compounds were tested in a formalin induced colonic inflammation model in BK:A mice. From these studies a trimodal compound based on a zinc Schiff base analogue of sulfasalazine was designed. This was tested against a trinitrobenzenesulfonic acid (TNB) induced colitic model in Wistar rats. The use of two models allows us to test our compounds in both an acute and a chronic model. The trimodal compound reported is observed to provide anticolitic properties in the chronic TNB induced colitis model commensurate with that of SASP. However, the design of trimodal compound still has the capacity for further development. This the platform reported may offer a route into compounds which can markedly outperform the anti-colitic properties of SASP.

Elucidation of the bonding of a near infrared dye to hollow gold nanospheres - a chalcogen tripod

Determining how Raman labels orientate on the surface of HGNs to aid in future advancements of designing NIR nanosensors.

Infrared surface enhanced Raman scattering (SERS) is an attractive technique for the in situ detection of nanoprobes in biological samples due to the greater depth of penetration and reduced interference compared to SERS in the visible region. A key challenge is to understand the surface layer formed in suspension when a specific label is added to the SERS substrate in aqueous suspension. SERS taken at different wavelengths, theoretical calculations, and surface-selective sum frequency generation vibrational spectroscopy (SFG-VS) were used to define the surface orientation and manner of attachment of a new class of infrared SERS labels with a thiopyrylium core and four pendant 2-selenophenyl rings. Hollow gold nanospheres (HGNs) were used as the enhancing substrate and two distinct types of SERS spectra were obtained. With excitation close to resonance with both the near infrared electronic transition in the label (max 826 nm) and the plasmon resonance maximum (690 nm), surface enhanced resonance Raman scattering (SERRS) was obtained. SERRS indicates that the major axis of the core is near to perpendicular to the surface plane and SFG-VS obtained from a dried gold film gave a similar orientation with the major axis at an angle 64–85° from the surface plane. Longer excitation wavelengths give SERS with little or no molecular resonance contribution and new vibrations appeared with significant displacements between the thiopyrylium core and the pendant selenophene rings. Analysis using calculated spectra with one or two rings rotated indicates that two rings on one end are rotated towards the metal surface to give an arrangement of two selenium and one sulphur atoms directly facing the gold structure. The spectra, together with a space filled model, indicate that the molecule is strongly adsorbed to the surface through the selenium and sulphur atoms in an arrangement which will facilitate layer formation.

Interaction of fluorescent dyes with DNA and spermine using fluorescence spectroscopy

Oligonucleotides labelled with fluorescent dyes are widely used as probes for the identification of DNA sequences in detection methods using optical spectroscopies such as fluorescence and surface enhanced Raman scattering (SERS). Spermine is widely used in surface enhanced based assays as a charge reduction and aggregating agent as it interacts strongly with the phosphate backbone and has shown to enhance the signal of a labelled oligonucleotide. The fluorescence intensity of two commonly used labels, FAM and TAMRA, were compared when spermine was added under different experimental conditions. There was a marked difference upon conjugating the free dye to an oligonucleotide, when FAM was conjugated to an oligonucleotide there was around a six fold decrease in emission, compared to a six fold increase when TAMRA was conjugated to an oligonucleotide. Dye labelled single and double stranded DNA also behaved differently with double stranded DNA labelled with FAM being a much more efficient emitter in the mid pH range, however TAMRA becomes increasingly less efficient as the pH rises. Upon addition of the base spermine, signal enhancement from the FAM labelled oligonucleotide is observed. Increasing probe concentrations of TAMRA oligonucleotide above 0.5 μM led to signal reduction most likely through quenching, either by an interaction with guanine, or through self-quenching. By using different bases for comparison, spermine and triethylamine (TEA), different affects were observed in the measured fluorescence signals. When TEA was added to FAM, a reduction in the pH dependence of fluorescence was observed, which may be useful for mid pH range assays. With the drive to increase information content and decrease time and complexity of DNA assays it is likely that more assays will be carried out in complex media such as extracted DNA fragments and PCR product. This model study indicates that dye DNA and dye spermine interactions are dye specific and that extreme care with conditions is necessary particularly if it is intended to determine the concentrations of multiple analytes using probes labelled with different dyes.

Determination of metal ion concentrations by SERS using 2,2′-bipyridyl complexes

SERS of bipyridyl complexes for the discrimination of six different metal ions.

Otolith microchemistry of tropical diadromous fishes: spatial and migratory dynamics

Otolith microchemistry was applied to quantify migratory variation and the proportion of native Caribbean stream fishes that undergo full or partial marine migration. Strontium and barium water chemistry in four Puerto Rico, U.S.A., rivers was clearly related to a salinity gradient; however, variation in water barium, and thus fish otoliths, was also dependent on river basin. Strontium was the most accurate index of longitudinal migration in tropical diadromous fish otoliths. Among the four species examined, bigmouth sleeper Gobiomorus dormitor, mountain mullet Agonostomus monticola, sirajo goby Sicydium spp. and river goby Awaous banana, most individuals were fully amphidromous, but 9-12% were semi-amphidromous as recruits, having never experienced marine or estuarine conditions in early life stages and showing no evidence of marine elemental signatures in their otolith core. Populations of one species, G. dormitor, may have contained a small contingent of semi-amphidromous adults, migratory individuals that periodically occupied marine or estuarine habitats (4%); however, adult migratory elemental signatures may have been confounded with those related to diet and physiology. These findings indicate the plasticity of migratory strategies of tropical diadromous fishes, which may be more variable than simple categorization might suggest.

A capture-recapture model of amphidromous fish dispersal

Adult movement scale was quantified for two tropical Caribbean diadromous fishes, bigmouth sleeper Gobiomorus dormitor and mountain mullet Agonostomus monticola, using passive integrated transponders (PITs) and radio-telemetry. Large numbers of fishes were tagged in Río Mameyes, Puerto Rico, U.S.A., with PITs and monitored at three fixed locations over a 2·5 year period to estimate transition probabilities between upper and lower elevations and survival probabilities with a multistate Cormack-Jolly-Seber model. A sub-set of fishes were tagged with radio-transmitters and tracked at weekly intervals to estimate fine-scale dispersal. Changes in spatial and temporal distributions of tagged fishes indicated that neither G. dormitor nor A. monticola moved into the lowest, estuarine reaches of Río Mameyes during two consecutive reproductive periods, thus demonstrating that both species follow an amphidromous, rather than catadromous, migratory strategy. Further, both species were relatively sedentary, with restricted linear ranges. While substantial dispersal of these species occurs at the larval stage during recruitment to fresh water, the results indicate minimal dispersal in spawning adults. Successful conservation of diadromous fauna on tropical islands requires management at both broad basin and localized spatial scales.

Silver and magnetic nanoparticles for sensitive DNA detection by SERS

The first reported combination of functionalised silver nanoparticles and silver-coated magnetic nanoparticles in a stable sandwich assay for DNA detection using SERS.

Surface enhanced resonance Raman scattering (SERRS)--a first example of its use in multiplex genotyping

Accurate multiplex genotyping of the mutational status of the cystic fibrosis gene with the sensitive and selective SERRS technique is reported. This new assay does not require separation of the various alleles and shows that SERRS is a realistic alternative detection technique for use in modern DNA assays.

Surface-enhanced Raman scattering (SERS) and surface-enhanced resonance Raman scattering (SERRS): a review of applications

Surface-enhanced Raman scattering (SERS) and surface-enhanced resonance Raman scattering (SERRS) can provide positive identification of an analyte or an analyte mixture with high sensitivity and selectivity. Better understanding of the theory and advances in the understanding of the practice have led to the development of practical applications in which the unique advantages of SERS/SERRS have been used to provide effective solutions to difficult analytical problems. This review presents a basic theory and illustrates the way in which SERS/SERRS has been developed for practical use.

Effects of Atenolol, Labetalol and Methyldopa on Endogenous Antioxidants In-vitro

The aim of this study was to investigate whether atenolol, labetalol and methyldopa, which are commonly used for the treatment of hypertension in pregnancy, can induce antioxidant activity.

Reactive oxygen species scavengers (plasma thiol, red cell lysate thiol, red cell superoxide dismutase, red cell membrane thiol and plasma glutathione) were measured after incubation of peripheral blood with atenolol and methyldopa, respectively.

The results showed that atenolol and labetalol could significantly raise the levels of plasma thiol and membrane thiol but had no effects on lysate thiol, superoxide dismutase and glutathione. The effects on membrane thiol occurred after 60 min incubation and on plasma thiol after 120 min incubation.

The data also suggest that atenolol and labetalol at lower concentrations tend to have additive effects on reactive oxygen species scavengers but at higher concentrations do not.

Methyldopa had no significant effect on any of the parameters measured.

These findings suggest that atenolol and labetalol are able to induce higher levels of antioxidant activity.

Dynamic Imaging Analysis of SERS-Active Nanoparticle Clusters in Suspension

A novel wide-field approach for the real-time Surface Enhanced Raman Scattering (SERS) imaging of multiple silver nanoparticle clusters suspended in solution is described. This method enables direct correlation of the SERS activity of a single nanoparticle aggregate and its size through measurement of the cluster diffusion coefficient and can also be performed in a high-throughput basis. As a first demonstration, we investigate the salt-induced aggregation of silver nanoparticles in the presence of a reporter tag molecule, which has a high affinity for the nanoparticle surface. In addition to tracking individual particles, direct comparison of Rayleigh and SERS videos of the same colloid solution enabled measurement of the fraction of individual clusters that are SERS active and the dependence of this value on the relative concentration of the tag molecule. Furthermore, given the ability to also rapidly profile any nonuniformity in particle size distributions, we expect this approach will not only provide a new tool for the fundamental understanding of SERS but also significantly contribute to the development of an array of emerging nanoparticle-enhanced biomolecule and imaging detection platforms.

THE NEOPLASTIC POTENTIALITIES OF MOUSE EMBRYO TISSUES : III. THE TUMORS ELICITED FROM GASTRIC EPITHELIUM

Epithelial tumors have been readily obtained by the implantation of embryo stomach tissue together with olive oil containing methylcholanthrene (with or without Scharlach R) in adult mice of homologous strain. The implanted tissue from the squamous portion of the stomach rapidly encysted the oil, and benign and malignant papillomas and squamous cell carcinomas soon arose from the stratified squamous lining of the cysts. Bits of the glandular portion of the stomach also formed cysts, but the gland cells underwent metaplasia in response to the carcinogen, altering first to transitional epithelium and then to a stratified squamous layer. So swiftly did these changes take place that nearly all of the tumors took origin from epithelium that had already become stratified and squamous, and the growths themselves were of this type. A single transitional cell carcinoma and an adenoacanthoma were procured, but no adenocarcinomas; nor did any benign papillomas develop, though they often resulted from the action of methylcholanthrene on the squamous portion of the embryo stomach. Search failed to disclose any distinctive precancerous changes in the gastric tissue. Five of the cancers were transplanted and they grew in every host. No tumors arose from any of the numerous control implants. Those consisting of glandular tissue formed cysts lined partly with columnar epithelium secreting mucus and partly with tubular glands equipped with chief and parietal cells in good condition. Pepsin and rennin were found in the fluid contained in these cysts, but no free hydrochloric acid. The enzymes were present also when the cysts contained methylcholanthrene and the glands had not yet been wholly replaced by metaplastic epithelium. The tumors appeared months sooner than when methylcholanthrene is injected into the stomach of adult animals or given by mouth; some of them were well established after 5 or 6 weeks. They arose regularly when the requisite experimental conditions were provided. The utilization of transplanted embryo tissue provides a means whereby gastric tumors free from bacterial infection can be procured swiftly and easily.

THE NEOPLASTIC POTENTIALITIES OF MOUSE EMBRYO TISSUES : I. THE FINDINGS WITH SKIN OF C STRAIN EMBRYOS TRANSPLANTED TO ADULT ANIMALS

A method has been devised whereby the transplanted epidermis of mouse embryos can be selectively exposed to the action of a chemical carcinogen. Scharlach R was dissolved in olive oil with the aim of stimulating and attracting the epidermal cells, methylcholanthrene was added to the solution, and numerous fine globules of it were injected into the thigh muscles of adult mice together with fragments of embryo skin. Much of the oil underwent primary inclusion in the resulting cysts, and the proliferating epidermis, while forming them, extended to not a few of the outlying droplets with result that they too were added to the cyst contents. During these activities the methylcholanthrene came into direct contact with many of the epithelial cells, and later on the layer lining the cyst was continually exposed to the influence of the carcinogen. The epidermis underwent neoplastic changes with great rapidity; often in less than 4 weeks papillomas and carcinomas had arisen like those deriving from adult epidermis. The growths were punctate in origin and usually multiple. Many were transplanted to adults of the same homologous breed of mice that furnished the embryo material (mice of C strain). The grafts did not uniformly succeed as was the case with those of normal skin of embryos of the same stock,-which regularly grew at first in the new hosts and remained alive long after. The benign papillomas failed to live or barely survived, and the apparently malignant papillomas, though rapidly forming nodules of considerable size, usually regressed later. Some of the carcinomas also regressed or wholly failed, while others gave rise to progressively enlarging tumors. The best results were obtained with grafts in which several neoplasms were intermingled, these flourishing together in the new hosts. Methylcholanthrene in olive oil exerts an influence on epidermal cells like that of Scharlach R, stimulating them to multiply, attracting them, and causing them to mimic carcinomatous elements.

THE NEOPLASTIC POTENTIALITIES OF MOUSE EMBRYO TISSUES : II. CONTRIBUTORY EXPERIMENTS; RESULTS WITH THE SKIN OF C3H AND WEBSTER-SWISS EMBRYOS; GENERAL CONSIDERATIONS

Experiments were carried out to learn whether the widely differing liabilities to induced epidermal tumors of individual mice and rabbits are due to a previous localization out of the blood of an agent capable of undergoing change when the skin is exposed to carcinogenic influences, and of producing tumors in consequence. On the assumption that such an agent would localize in increased quantity where cutaneous inflammation exists, like various inert substances of large molecule and the epidermotrophic viruses when circulating, skin areas on adult and new-born animals were for some weeks kept inflamed, and months later, when the areas appeared normal, methylcholanthrene was applied to them and to control areas on the same or other individuals. No differences were observable in tumor incidence. These results led to attempts to test whether embryo epidermis is capable of undergoing neoplastic change, and the work of Paper I was done which showed that epidermal tumors arise with great rapidity and regularity from embryo skin transplanted to adults of homologous strain (C strain) together with methylcholanthrene. Webster-Swiss mice proved unsuited to experiments of the sort owing to heterogeneity of the breed, the transplanted embryo skin dying in most instances before the methylcholanthrene introduced with it could have been carcinogenic. The skin of C3H embryos also did badly, as if from incompatibility in some instances but mostly because its epidermal cells proliferated less vigorously than those of C embryos and did not tolerate methylcholanthrene nearly so well. Despite these difficulties, epidermal tumors were occasionally induced, as also in the transplanted skin of Webster-Swiss embryos, and the growths appeared quite soon, all things considered. The effect of methylcholanthrene on the skin of sucklings, their mothers, and young adult mice of the C strain was studied in order to find out whether the rapid rate of neoplastic change in the transplanted epidermis of embryos is indicative of some liability connected with its period of development. The skin of new-born animals proved very refractory to the carcinogen, hair coming in at the same rate as on control litters and no perceptible inflammation occurring for about 2 weeks, although within this period the mothers of the treated animals and the young adults became hairless where the methylcholanthrene had been put and their skin was much inflamed. Later on, as the applications were kept up, similar changes took place in the sucklings, but none of these developed tumors during some 6 weeks of observation whereas growths appeared within 3 weeks on more than half of the mother mice and on some of the young adults. The failure to produce tumors in the sucklings seems to have been due to cutaneous conditions preventing the necessary exposure of the deeper epidermal cells to methylcholanthrene. In any projected correlation of age differences with the response of cells to carcinogens allowance must be made for such factors. The present findings give no ground for the supposition that embryo skin has any special liability to neoplastic change. The results of transferring the tumors derived from embryo epidermis to new hosts have made plain that the neoplastic state not infrequently entails disabilities which are crucial, the tumor cells failing to succeed unless aided. This holds true of some carcinomas as well as of papillomas. By transplanting pieces of the organs of C embryos together with methylcholanthrene tumors of many sorts besides the epidermal have been obtained. As yet only those of the stomach have been worked with extensively. They can be elicited as quickly and regularly as those of the epidermis and can be as easily transplanted. The findings as a whole render it impossible to suppose that the neoplastic potentialities possessed by transplanted embryo tissues are due to the lodgement in them of tumor-producing viruses as specialized in their effects as those now known, or of precursor agents conferring neoplastic liabilities specialized to the same degree. Some other possibilities are mentioned. The rarity of neoplasms at birth is due to the circumstances of intrauterine life and to its brevity, not to any lack of capacity of the cells of the embryo to undergo neoplastic change.

Short-wave infrared excited SERS

Optimisation of colloidal properties allows Surface Enhanced Raman Scattering (SERS) to be recorded from a range of analytes at 1546 nm, demonstrating the potential of SERS for use in a wavelength region of particular value for applications such as homeland security.

Electron energy-loss spectroscopy (EELS) of surface plasmons in single silver nanoparticles and dimers: influence of beam damage and mapping of dark modes

We demonstrate the use of a scanning transmission electron microscope (STEM) equipped with a monochromator and an electron energy loss (EEL) spectrometer as a powerful tool to study localized surface plasmons in metallic nanoparticles. We find that plasmon modes can be influenced by changes in nanostructure geometry and electron beam damage and show that it is possible to delineate the two effects through optimization of specimen preparation techniques and acquisition parameters. The results from the experimental mapping of bright and dark plasmon energies are in excellent agreement with the results from theoretical modeling.

Characterization of active site structure in CYP121. A cytochrome P450 essential for viability of Mycobacterium tuberculosis H37Rv

Mycobacterium tuberculosis (Mtb) cytochrome P450 gene CYP121 is shown to be essential for viability of the bacterium in vitro by gene knock-out with complementation. Production of CYP121 protein in Mtb cells is demonstrated. Minimum inhibitory concentration values for azole drugs against Mtb H37Rv were determined, the rank order of which correlated well with Kd values for their binding to CYP121. Solution-state spectroscopic, kinetic, and thermodynamic studies and crystal structure determination for a series of CYP121 active site mutants provide further insights into structure and biophysical features of the enzyme. Pro346 was shown to control heme cofactor conformation, whereas Arg386 is a critical determinant of heme potential, with an unprecedented 280-mV increase in heme iron redox potential in a R386L mutant. A homologous Mtb redox partner system was reconstituted and transported electrons faster to CYP121 R386L than to wild type CYP121. Heme potential was not perturbed in a F338H mutant, suggesting that a proposed P450 superfamily-wide role for the phylogenetically conserved phenylalanine in heme thermodynamic regulation is unlikely. Collectively, data point to an important cellular role for CYP121 and highlight its potential as a novel Mtb drug target.

Control of enhanced Raman scattering using a DNA-based assembly process of dye-coded nanoparticles

Enhanced Raman scattering from metal surfaces has been investigated for over 30 years. Silver surfaces are known to produce a large effect, and this can be maximized by producing a roughened surface, which can be achieved by the aggregation of silver nanoparticles. However, an approach to control this aggregation, in particular through the interaction of biological molecules such as DNA, has not been reported. Here we show the selective turning on of the surface enhanced resonance Raman scattering effect on dye-coded, DNA-functionalized, silver nanoparticles through a target-dependent, sequence-specific DNA hybridization assembly that exploits the electromagnetic enhancement mechanism for the scattering. Dye-coded nanoparticles that do not undergo hybridization experience no enhancement and hence do not give surface enhanced resonance Raman scattering. This is due to the massive difference in enhancement from nanoparticle assemblies compared with individual nanoparticles. The electromagnetic enhancement is the dominant effect and, coupled with an understanding of the surface chemistry, allows surface enhanced resonance Raman scattering nanosensors to be designed based on a natural biological recognition process.

Surface-enhanced Raman scattering spectroscopy as a sensitive and selective technique for the detection of folic acid in water and human serum

Surface-enhanced Raman scattering (SERS) is shown to give linear and sensitive concentration-dependent detection of folic acid using silver nanoparticles created via ethylene-diaminetetraacetic acid (EDTA) reduction. Optical detection by SERS overcomes the primary limitation of photodissociation encountered during the application of other shorter wavelength ultraviolet (UV)/near-UV techniques such as fluorescence based microscopy. The SERS approach in water-based samples was demonstrated and optimized using several longer wavelengths of excitation (514.5, 632.8, and 785 nm). Excitation in the green (514.5 nm) was found to achieve the best balance between photodissociation and SERS efficiency. Linear concentration dependence was observed in the range of 0.018 to 1 microM. The importance of folic acid in a clinical setting and the potential applications of this technique in a biological environment are highlighted. We demonstrate the potential to transfer this technique to real biological samples by the detection of folic acid in human serum samples by SERS.

Ultrasensitive DNA detection using oligonucleotide-silver nanoparticle conjugates

Oligonucleotide-gold nanoparticle (OGN) conjugates are powerful tools for the detection of target DNA sequences due to the unique properties conferred upon the oligonucleotide by the nanoparticle. Practically all the research and applications of these conjugates have used gold nanoparticles to the exclusion of other noble metal nanoparticles. Here we report the synthesis of oligonucleotide-silver nanoparticle (OSN) conjugates and demonstrate their use in a sandwich assay format. The OSN conjugates have practically identical properties to their gold analogues and due to their vastly greater extinction coefficient both visual and absorption analyses can occur at much lower concentrations. This is the first report of OSN conjugates being successfully used for target DNA detection and offers improved sensitivity which is of interest to a range of scientists.

Analysis of the interactions of cytochrome b5 with flavocytochrome P450 BM3 and its domains

Interactions between a soluble form of microsomal cytochrome b(5) (b(5)) from Musca domestica (housefly) and Bacillus megaterium flavocytochrome P450 BM3 and its component reductase (CPR), heme (P450) and FAD/NADPH-binding (FAD) domains were analyzed by a combination of steady-state and stopped-flow kinetics methods, and optical spectroscopy techniques. The high affinity binding of b(5) to P450 BM3 induced a low-spin to high-spin transition in the P450 heme iron (K(d) for b(5) binding = 0.44 microM and 0.72 microM for the heme domain and intact flavocytochrome, respectively). The b(5) had modest inhibitory effects on steady-state turnover of P450 BM3 with fatty acids, and the ferrous-carbon monoxy P450 complex was substantially stabilized on binding b(5). Single turnover reduction of b(5) by BM3 using stopped-flow absorption spectroscopy (k(lim) = 116 s(-1)) was substantially faster than steady-state reduction of b(5) by P450 BM3 (or its CPR and FAD domains), indicating rate-limiting step(s) other than BM3 flavin-to-b(5) heme electron transfer in the steady-state reaction. Steady-state b(5) reduction by P450 BM3 was considerably accelerated at high ionic strength. Pre-reduction of P450 BM3 by NADPH decreased the k(lim) for b(5) reduction approximately 10-fold, and also resulted in a lag phase in steady-state b(5) reduction that was likely due to BM3 conformational perturbations sensitive to the reduction state of the flavocytochrome. Ferrous b(5) could not reduce the ferric P450 BM3 heme domain under anaerobic conditions, consistent with heme iron reduction potentials of the two proteins. However, rapid oxidation of both hemoproteins occurred on aeration of the ferrous protein mixture (and despite the much slower autoxidation rate of b(5) in isolation), consistent with electron transfer occurring from b(5) to the oxyferrous P450 BM3 in the complex. The results demonstrate that strong interactions occur between a eukaryotic b(5) and a model prokaryotic P450. Binding of b(5) perturbs BM3 heme iron spin-state equilibrium, as is seen in many physiologically relevant b(5) interactions with eukaryotic P450s. These results are consistent with the conservation of structure of P450s (particularly at the heme proximal face) between prokaryotes and eukaryotes, and may point to as yet undiscovered roles for b(5)-like proteins in the control of activities of certain prokaryotic P450s.

Quantitative enhanced Raman scattering of labeled DNA from gold and silver nanoparticles

Surface-enhanced resonance Raman scattering (SERRS) from silver nanoparticles using 514.5-nm excitation has been shown to offer huge potential for applications in highly sensitive multiplexed DNA assays. If the technique is to be applied to real biological samples and integrated with other methods, then the use of gold nanoparticles and longer wavelengths of excitation are desirable. The data presented here demonstrate that dye-labeled oligonucleotide sequences can be directly detected by SERRS using gold nanoparticles in a quantitative manner for the first time. The performance of gold and silver nanoparticles as SERRS substrates was assessed using 514.5-, 632.8-, and 785-nm excitation and a range of 13 commercially available dye-labeled oligonucleotides. The quantitative response allowed the limit of detection to be determined for each case and demonstrates that the technique is highly effective, sensitive, and versatile. The possibility of excitation at multiple wavelengths further enhances the multiplexing potential of the technique. The importance of effectively combining the optical properties of the nanoparticle and the dye label is demonstrated. For example, at 632.8-nm excitation, the dye BODIPY TR-X and gold nanoparticles make a strong SERRS combination with very little background fluorescence. This study allows the choice of nanoparticle and dye label for particular experimental setups, and significantly expands the applicability of enhanced Raman scattering for use in many disciplines.

Enhanced oligonucleotide-nanoparticle conjugate stability using thioctic acid modified oligonucleotides

Metallic nanoparticles of gold functionalized with oligonucleotides conventionally use a terminal thiol modification and have been used in a wide range of applications. Although readily available, the oligonucleotide–nanoparticle conjugates prepared in this way suffer from a lack of stability when exposed to a variety of small molecules or elevated temperatures. If silver is used in place of gold then this lack of stability is even more pronounced. In this study we report the synthesis of highly stabilized oligonucleotide–nanoparticle conjugates using a simple oligonucleotide modification. A modified solid support was used to generate 3′-thioctic acid modified oligonucleotides by treatment with an N-hydroxysuccimidyl ester of thioctic acid. Unusually, both gold and silver nanoparticles have been investigated in this study and show that these disulphide-modified oligonucleotide probes offer significant improvements in nanoparticle stability when treated with dithiothreitol (DTT) compared with monothiol analogues. This is a significant advance in oligonucleotide–nanoparticle conjugate stability and for the first time allows silver nanoparticles to be prepared that are more stable than standard gold-thiol functionalized nanoparticles. This opens up the possibility of using silver nanoparticles functionalized with oligonucleotides as an alternative to gold.

Bead-Based DNA Diagnostic Assay for Chlamydia Using Nanoparticle-Mediated Surface-Enhanced Resonance Raman Scattering Detection within a Lab-on-a-Chip Format

There is a continued interest in the development of new on-chip protocols for the determination of the causes of infectious disease. In this paper, we demonstrate the use of surface-enhanced resonance Raman scattering (SERRS) for detecting the clinically relevant nucleic acid sequences of Chlamydia trachomatis in a bead-based lab-on-a-chip format, incorporating a solid-phase sample clean-up on-chip. The assay uses streptavidinated polymer microspheres to capture a biotinylated PCR product of the oligonucleotide sequence, which was subsequently hybridized against a complementary rhodamine-labeled, Raman active probe. Central to the assay is an in-channel integrated microfilter, which was used to retain the microspheres, enabling the bound target to be separated from the rest of the sample as part of a solid-phase clean-up (thereby removing any contributions from the background). After washing, the bound Rhodamine labeled detection probe was released thermally from the microspheres by heating and was subsequently mixed on-chip with a stream of silver nanoparticles. The signal was detected downstream using a Raman spectrometer to collect the SERRS response. The assay offers several advantages over traditional laboratory methods, including: the speed of the assay on-chip, the potential for sample clean-up; and the low volume of sample required.

TNT stilbene derivatives as SERRS active species

Synthesis of four trinitrotoluene stilbene derivatives and assessment for SERRS activity is reported.

Single molecule level detection of allophycocyanin by surface enhanced resonance Raman scattering

Single molecule level detection of the near-infrared fluorescent protein allophycocyanin (APC) has been achieved using surface enhanced resonance Raman scattering (SERRS). The detection limit using the peak height of the 440 cm(-1) band was 1 x 10(-13) mol l(-1), compared to 2 x 10(-12) mol l(-1) for the fluorescence peak at 660 nm.

Highly sensitive detection of dye-labelled DNA using nanostructured gold surfaces

Careful control of surface chemistry results in strong surface enhanced resonance Raman scattering from dye-labelled oligonucleotides assembled on nanostructured gold surfaces, releasing their potential as reliable enhancing surfaces.

Protein–nanoparticle labelling probed by surface enhanced resonance Raman spectroscopy

A benzotriazole dye has been attached to a heme protein via a Michael addition and the unique potential of surface enhanced resonance Raman scattering (SERRS) to provide informative in situ recognition of more than one label on one protein demonstrated.

A TEM and electron energy loss spectroscopy (EELS) investigation of active and inactive silver particles for surface enhanced resonance Raman spectroscopy (SERRS)

A number of silver particles and aggregates of particles were studied using surface enhanced resonance Raman spectroscopy (SERRS), high resolution transmission electron microscopy (HRTEM) and electron energy-loss spectroscopy (EELS). The SERRS mapping/TEM collage method developed previously in our group allows each SERRS active or inactive species to be reliably identified and analysed by each of the techniques in three different instruments. Our aim is to correlate SERRS activity, particle microstructure, chemical composition and electronic properties of each species to gain an insight into the enhancement mechanism. To date, our findings do not reveal any clear link between particle microstructure and SERRS activity. Additionally, the direction of the polarisation of the incident excitation or the presence of interparticle junctions between aggregated particles was not correlated with SERRS activity. However, spectral variations in the EELS data from structurally similar particles and SERRS active and inactive particles suggest that each species is chemically/electronically distinct. Differences in the spectra of single particles, dimers and clusters were also observed. Further analysis of the data, including extraction of the complex dielectric function from the EELS data, will provide an insight into the relationship between these observations and SERRS activity.

Biosensing using silver nanoparticles and surface enhanced resonance Raman scattering

Silver nanoparticles can be used to provide excellent surface enhanced resonance Raman scattering. Control of the surface chemistry and the use of appropriate protocols enables effective sensing of biomolecules.

A new approach for DNA detection by SERRS

A new approach for the detection of DNA using surface enhance resonance Raman scattering (SERRS) is reported. The majority of existing techniques use fluorescence spectroscopy with advanced probe design to provide information on the identity of specific DNA sequences down to single base resolution. A new approach to the labelling of DNA is discussed which uses Michael addition to couple thiolated DNA to dye labels specifically designed to attach to silver surfaces. When combined with existing strategies for sensitive detection of DNA using commercially available labels, a new class of biomolecular probe known as a SERRS Beacon was produced. The detection techniques of fluorescence and surface enhanced resonance Raman scattering (SERRS) are combined to give a sensitive and selective system for use in the development and creation of novel assays for specifically defined targets. It demonstrates improved potential for multiplexing analysis.