Alkylresorcinol detection and identification in archaeological pottery using ultra-high-performance liquid chromatography-quadrupole/Orbitrap mass spectrometry

RATIONALE

Alkylresorcinols (AR) are cereal-specific biomarkers and have recently been found in archaeological pots. However, their low concentrations and high susceptibility to degradation make them difficult to detect using conventional gas chromatography mass spectrometry (GC/MS). Here we describe the development of a more sensitive liquid chromatography mass spectrometry (LC/MS) method to detect these compounds.

METHOD

A method based on the use of ultra-high-performance liquid chromatography (UHPLC) coupled to an Orbitrap mass analyser was established and validated for the detection of low-concentration ARs in pottery. During the preliminary experiments, UHPLC-Q/Orbitrap MS (ultra-high-performance liquid chromatography-quadrupole/Orbitrap mass spectrometry) was demonstrated to be more sensitive, and a wide range of AR homologues in cereal extracts were detected, unlike UHPLC-QTOFMS (ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry) and GC/MS. The developed method was utilised to profile AR homologue distribution in modern cereal samples and reanalyse AR-containing pots from the archaeological site of Must Farm.

RESULTS

A highly sensitive LC/MS method with a limit of detection (LOD) of 0.02 μg/g and a limit of quantification (LOQ) of 0.06 μg/g was used to profile ARs in five modern cereal grains. The obtained LOD is 250 times lower than that obtained using the conventional GC/MS approach. AR 21:0 was the most abundant homologue in all four Triticum spp.-einkorn, emmer, Khorasan wheat and common wheat. Meanwhile, AR 25:0 was the predominant homologue in barley, potentially enabling differentiation between wheat and barley. The developed LC/MS-based method was successfully used to analyse ARs extracted from Must Farm potsherds and identified the cereal species most likely processed in the pots-emmer wheat.

CONCLUSION

The described method offers an alternative and more sensitive approach for detecting and identifying ARs in ancient pottery. It has been successfully utilised to detect AR homologues in archaeological samples and discriminate which cereal species-wheat and barley-were processed in the pots.

Polarisation-sensitive optical coherence tomography measurement of retardance in fibrosis, a non-invasive biomarker in patients with systemic sclerosis

Polarisation-sensitive optical coherence tomography (PS-OCT) offers a novel, non-invasive method of assessing skin fibrosis in the multisystem disease systemic sclerosis (SSc) by measuring collagen retardance. This study aimed to assess retardance as a biomarker in SSc. Thirty-one patients with SSc and 27 healthy controls (HC) underwent PS-OCT imaging. 'Skin score' was assessed by clinical palpation (0-3 scale). A subset of ten patients and ten age/sex-matched HC had a biopsy and longitudinal imaging. Histological assessment included quantification of epidermal thickness, collagen content (to assess fibrosis) and matrix metalloproteinase (MMP) activity (in situ zymography). PS-OCT images were assessed for epidermal thickness (structure) and fibrosis (retardance). Positive correlation was observed between epidermal thickness as measured by histology and structural PS-OCT (r = 0.79; p < 0.001). Retardance was: HC mean 0.21 (SD 0.21) radian/pixel; SSc skin score 0, 0.30 (0.19); skin score 1, 0.11 (0.16); skin score 2, 0.06 (0.12); skin score 3, 0.36 (0.35). Longitudinal retardance decreased at one-week across groups, increasing at one-month for HC/skin score 0-1; HC biopsy site retardance suggests scarring is akin to fibrosis. Relationships identified between retardance with both biopsy and skin score data indicate that retardance warrants further investigation as a suitable biomarker for SSc-related fibrosis.

Estimating the dwarfing rate of an extinct Sicilian elephant

Evolution on islands, together with the often extreme phenotypic changes associated with it, has attracted much interest from evolutionary biologists. However, measuring the rate of change of phenotypic traits of extinct animals can be challenging, in part due to the incompleteness of the fossil record. Here, we use combined molecular and fossil evidence to define the minimum and maximum rate of dwarfing in an extinct Mediterranean dwarf elephant from Puntali Cave (Sicily).¹ Despite the challenges associated with recovering ancient DNA from warm climates,² we successfully retrieved a mitogenome from a sample with an estimated age between 175,500 and 50,000 years. Our results suggest that this specific Sicilian elephant lineage evolved from one of the largest terrestrial mammals that ever lived³ to an island species weighing less than 20% of its original mass with an estimated mass reduction between 0.74 and 200.95 kg and height reduction between 0.15 and 41.49 mm per generation. We show that combining ancient DNA with paleontological and geochronological evidence can constrain the timing of phenotypic changes with greater accuracy than could be achieved using any source of evidence in isolation.

Author Correction: The dental proteome of Homo antecessor

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Ancient DNA (aDNA) sequencing has enabled reconstruction of speciation, migration, and admixture events for extinct taxa¹. Outside the permafrost, however, irreversible aDNA post-mortem degradation² has so far limited aDNA recovery to the past ~0.5 million years (Ma)³. Contrarily, tandem mass spectrometry (MS) allowed sequencing ~1.5 million year (Ma) old collagen type I (COL1)⁴ and suggested the presence of protein residues in Cretaceous fossil remains⁵, although with limited phylogenetic use⁶. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae^7–9 using a ~1.77 Ma old dental enamel proteome of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)¹⁰. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that the latter includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference. It also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates¹¹, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.

Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities

Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These 'soft tissues' have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil 'soft tissues' differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.

Continuously rotating chiral liquid crystal droplets in a linearly polarized laser trap

The transfer of optical angular momentum to birefringent particles via circularly polarized light is common. We report here on the unexpected, continuous rotation of chiral nematic liquid crystal droplets in a linearly polarized optical trap. The rotation is non-uniform, occurs over a timescale of seconds, and is observed only for very specific droplet sizes. Synchronized vertical motion of the droplet occurs during the rotation. The motion is the result of photo-induced molecular reorganization, providing a micron sized opto-mechanical transducer that twists and translates.

A novel modelling and experimental technique to predict and measure tissue temperature during CO2 laser stimuli for human pain studies

Laser nerve stimulation is now accepted as one of the preferred methods for applying painful stimuli to human skin during pain studies. One of the main concerns, however, is thermal damage to the skin. We present recent work based on using a CO2 laser with a remote infrared (IR) temperature sensor as a feedback system. A model for predicting the subcutaneous skin temperature derived from the signal from the IR detector allows us to accurately predict the laser parameters, thus maintaining an optimum pain stimulus whilst avoiding dangerous temperature levels, which could result in thermal damage. Another aim is to relate the modelling of the CO2 fibre laser interaction to the pain response and compare these results with practical measurements of the pain threshold for various stimulus parameters. The system will also allow us to maintain a constant skin temperature during the stimulus. Another aim of the experiments underway is to review the psychophysics for pain in human subjects, permitting an investigation of the relationship between temperature and perceived pain.

Depth-resolved holographic imaging through scattering media by use of a photorefractive polymer composite device in the near infrared

We report full-field depth-resolved holographic imaging through scattering media by use of a photorefractive polymer device in the near infrared. Real-time images through seven scattering mean free paths are acquired in a few seconds with a broadband superluminescent diode at 794 nm. A depth resolution of 15 microm and a transverse resolution of better than 42 microm are achieved. The photorefractive devices used are based on a poly(N-vinylcarbazole):2,4,7-trinitro-9-fluorenone dimalenitrile charge-transport network doped with the electro-optic chromophore 1-(2'-ethylhexyloxy)-2,5-dimethyl-4-(4"-nitrophenylazo)benzene.

Thermal effects of the Er:YAG laser on a simulated dental pulp: a quantitative evaluation of the effects of a water spray

OBJECTIVES

To quantify the temperature increments in a simulated dental pulp following irradiation with an Er:YAG laser, and to compare those increments when the laser is applied with and without water spray.

METHODS

Two cavities were prepared on either the buccal or lingual aspect of sound extracted teeth using the laser. One cavity was prepared with water spray, the other without and the order of preparation randomised. Identical preparation parameters were used for both cavities. Temperature increments were measured in the pulp chamber using a calibrated thermocouple and a novel pulp simulant.

RESULTS

Maximum increments were 4.0 degrees C (water) and 24.7 degrees C (no water). Water was shown to be highly significant in reducing the overall temperature increments in all cases (p<0.001; paired t-test). None of the samples prepared up to a maximum of 135 J cumulative energy prepared with water spray exceeded that threshold at which pulpal damage can be considered to occur. Only 25% of those prepared without water spray remained below this threshold.

DISCUSSION

Extrapolation of the figures suggests probably tolerable limits of continuous laser irradiation with water in excess to 160 J. With the incorporation of small breaks in the continuity of laser irradiation that occur in the in vivo situation, the cumulative energy dose tolerated by the pulp should far exceed these figures.

CONCLUSIONS

The Er:YAG laser must be used in conjunction with water during cavity preparation. As such it should be considered as an effective tool for clinical use based on predicted pulpal responses to thermal stimuli.

Laser-tissue interaction with a continuous wave 3-mcm fibre laser: preliminary studies with soft tissue

BACKGROUND AND OBJECTIVE

Lasers operating at wavelengths in the mid-infrared region have become increasingly popular for applications in areas of surgery and medicine. Advances in fibre laser technology have introduced a highly efficient, compact, diode-pumped source operating at around the 3-mcm wavelength. This study examines the effects of this recently developed laser on soft biological tissue.

STUDY DESIGN/MATERIALS AND METHODS

Chicken breast and liver tissue samples were exposed to 800 mW continuous wave laser power, at a wavelength of 2.71 mcm, with incident spot sizes of around 150 mcm. Samples were inspected grossly immediately after laser irradiation and also prepared for histologic processing.

RESULTS

After irradiation, visual assessment of changes at sample surfaces indicated a region of thermally affected tissue surrounding the ablation crater. This region was observed to grow in size to around 1.0 mm in diameter after 3 seconds of laser exposure at 800 mW. An ablation velocity of 0.80 mm.s(-1) was determined in chicken breast for the same incident laser parameters. Analysis of samples irradiated at 800 mW and processed for histology revealed minimal damage at hole boundaries and no signs of char formation, providing incident exposure times were restricted to below around 0. 5 seconds.

CONCLUSION

This fibre laser source has demonstrated its potential to fulfil medical applications, enabling accurate, precise tissue removal to proceed at a rapid ablation rate. The efficiency and small size of the laser are attractive features.

Pattern of healing of calvarial bone in the rat following application of the erbium-YAG laser

BACKGROUND AND OBJECTIVE

The aim of this study was to examine the pattern of healing in rat calvarial defects prepared with the erbium-YAG laser, using the "guided tissue regeneration" technique [Dahlin et al., Scand J Plast Reconstr Hand Surg 1990;24: 13-19].

STUDY DESIGN/MATERIALS AND METHODS

PTFE membranes were placed over the lased skull defects and the skin wounds sutured. Rats were killed humanely at intervals after surgery and the skulls processed for paraffin wax histology. A further group of mature rats was killed humanely and the calvariae removed. Slots were prepared using the erbium-YAG laser and immediately examined under the environmental scanning electron microscope (ESEM) in hydrated conditions, which avoided drying artefact.

RESULTS

An amorphous, mineral-rich carbon layer surrounds the lased bone defect, which in the in vivo experiments was seen as a basophilic zone that was resistant to resorption.

CONCLUSION

Bone infilling of the lased defect was retarded by delayed resorption of the amorphous, mineral-rich carbon layer.

Laser-tissue interaction with a high-power 2-microm fiber laser: preliminary studies with soft tissue

BACKGROUND AND OBJECTIVE

Recent developments in fiber laser technology have introduced highly efficient, compact sources with high output beam quality. The first laser-tissue interaction studies with a high-power 2-microm fiber laser were conducted.

STUDY DESIGN/MATERIALS AND METHODS

Chicken breast and porcine muscle tissue samples were subjected to continuous wave (cw) irradiation at 800-mW and 5-W output power levels, with spot sizes of approximately 150 microm. After laser irradiation, samples were inspected with an optical microscope and prepared for histologic processing.

RESULTS

Evaluation of surface changes in tissue samples indicated an interaction similar in nature to those previously demonstrated with other cw lasers, but with photothermal ablation characteristics typical of strongly absorbed lasers operating in the infrared wavelength region. An ablation velocity of 0.27 mm.sec(-1) in porcine tissue was determined at 800-mW incident power. Histopathologic analysis demonstrated the formation of lesions with minimal damage at boundaries and no evidence of carbonization.

CONCLUSIONS

Results indicate that this fiber laser has the potential to fulfill applications in the medical field.

Osseointegration of titanium metal implants in erbium-YAG laser-prepared bone

Titanium screws were implanted in rat calvarial defects of identical size using either a laser or bur. The aims of this study were to determine whether the screws were able to osseointegrate in a laser-prepared bone defect and to compare the pattern of bone healing around these screws. The optimal laser settings to produce a 0.7-mm-diameter hole in the rat calvaria were determined. A 0.7-mm-diameter hole was prepared on the left calvaria with the erbium-YAG laser to receive a 1-mm-diameter self-threading titanium screw. Each animal also received a 0.7-mm-diameter hole prepared on the right calvaria with a conventional metal bur, and a 1-mm-diameter self-threading screw implant was placed. Rats were killed humanely either 3 weeks or 3 months after surgery, and the skulls were processed in paraffin wax for histological analysis. Laser-prepared defects: At 3 weeks, the screw was surrounded by vital woven bone. The dura mater was perforated, and cystic change was present in the underlying brain tissue. There was active bone formation adjacent to the screw surface, deposited on a thin zone of necrotic bone. At 3 months, the screws were osseointegrated, and the brain tissue was healed by gliosis. Bur-prepared defects: At 3 weeks, there was extensive remodeling around the prepared defect. The dura mater was intact, and there was no damage to the underlying brain. At 3 months, the screws were successfully osseointegrated with bone adjacent to the screw. Osseointegration of titanium screws can be achieved using an erbium-YAG laser to prepare the implant bed.

Etch rate and spectroscopic ablation studies of Er:YAG laser-irradiated dentine

The interaction of a 200-mus Er:YAG laser at 2.94 mum with human molar dentine has been studied by ablation depth rate measurements as well as time-resolved and optical multichannel analyzer emission spectroscopy. Ablation rates indicate a threshold fluence of ~5.2 J cm(-2) for significant material removal with a low-fluence (<20 J cm(-2)) effective optical absorption coefficient of ~700 cm(-1). Deviation from a Beer's law dependence is significant in the range ~20 to ~60 J cm(-2) and indicates a maximum effective plume absorption of ~1200 cm(-1) at ~40 J cm(-2), coinciding with the appearance of strong line and broadband optical emission in the visible region. Time-of-flight emission measurements yield maximum species-resolved ablation velocities of up to ~1.2 x 10(6) cm s(-1), enabling calculation of plasma temperatures. The results suggest that etch-rate characteristics are driven by changes in plume absorption dynamics, which have a strong dependency on incident laser fluence.

Identification of photoacoustic transients during pulsed laser ablation of the human temporal bone: an experimental model

Laser ablation of hard tissues during neurotologic operations has been accomplished with continuous-wave (CW) lasers in the visible and midinfrared spectrum. The mechanism of ablation at these wavelengths is secondary to photothermal-induced tissue destruction. As a result, significant thermal damage to surrounding tissue may occur. Pulsed ultraviolet (UV) lasers have been suggested as an alternative to the argon, KTP-532, and CO2 lasers currently used in clinical practice. The pulse length of Excimer lasers are considerably shorter than the thermal diffusion time of bone tissue, and as a consequence thermal injury is minimal. This makes pulsed lasers an attractive tool for tissue ablation in the ear: in essence a "cold knife." However, the short pulse width of Excimer lasers (typically 10-150 ns) can create large thermoelastic stresses in the ablation specimen. This study identifies the presence of these photoacoustic waves during the Excimer laser treatment of the cadaveric human temporal bone. A XeCl (lambda = 308 nm, tau p = 12 ns) excimer laser was used to ablate hard tissue surrounding the oval window and facial ridge with energies of 75, 45, 25, and 12 mJ/pulse. Spot size was estimated to be 0.5 mm2. Custom high-frequency polyvinyldifluoride (PVDF) piezoelectric film transducers were fabricated and attached to the promontory, round window niche, and facial ridges. The signals were amplified using a low-noise preamplifier and recorded on a digitizing oscilloscope. Photoacoustic waves were clearly identified. Notably, large acoustic waves were measured on the promontory and on both sides of the facial ridge. The implications and clinical relevance of these findings is discussed and compared to findings obtained from a model system.

Brief communication: sliding displacement of amnion and chorion following controlled laser wounding suggests a mechanism for short-term sealing of ruptured membranes

The Erbium-YAG laser was used to produce narrow wounds of defined depth in term amniochorion. The charring effect of the laser meant that sites could be readily localized in histological sections. During brief post-wounding incubations, sliding displacement of the amnion relative to the chorion occurred through the plane of the spongy layer. This suggests a possible short-term mechanism whereby a spontaneous rupture could be sealed in vivo.