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.

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

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.

The foot of Homo naledi.

Modern humans are characterized by a highly specialized foot that reflects our obligate bipedalism. Our understanding of hominin foot evolution is, although, hindered by a paucity of well-associated remains. Here we describe the foot of Homo naledi from Dinaledi Chamber, South Africa, using 107 pedal elements, including one nearly-complete adult foot. The H. naledi foot is predominantly modern human-like in morphology and inferred function, with an adducted hallux, an elongated tarsus, and derived ankle and calcaneocuboid joints. In combination, these features indicate a foot well adapted for striding bipedalism. However, the H. naledi foot differs from modern humans in having more curved proximal pedal phalanges, and features suggestive of a reduced medial longitudinal arch. Within the context of primitive features found elsewhere in the skeleton, these findings suggest a unique locomotor repertoire for H. naledi, thus providing further evidence of locomotor diversity within both the hominin clade and the genus Homo.

1064 nm SERS of NIR active hollow gold nanotags.

Surface enhanced Raman scattering (SERS) tags are in situ probes that can provide sensitive and selective probes for optical analysis in biological materials. Engineering tags for use in the near infrared (NIR) region is of particular interest since there is an uncongested spectral window for optical analysis due to the low background absorption and scattering from many molecules. An improved synthesis has resulted in the formation of hollow gold nanoshells (HGNs) with a localised surface plasmon resonance (LSPR) between 800 and 900 nm which provide effective SERS when excited at 1064 nm. Seven Raman reporters containing aromatic amine or thiol attachment groups were investigated. All were effective but 1,2-bis(4-pyridyl)ethylene (BPE) and 4,4-azopyridine (AZPY) provided the largest enhancement. At approximately monolayer coverage, these two reporters appear to pack with the main axis of the molecule perpendicular or nearly perpendicular to the surface giving strong SERS and thus providing effective 1064 nm gold SERS nanotags.

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.

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.

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.

Isolation of "Candidatus Rickettsia andeanae" (Rickettsiales: Rickettsiaceae) in embryonic cells of naturally infected Amblyomma maculatum (Ixodida: Ixodidae).

The Gulf Coast tick, Amblyomma maculatum Koch, has become increasingly important in public health for its role as a vector of the recently recognized human pathogen, Rickettsia parkeri. More recently, these ticks were also found to harbor a novel spotted fever group rickettsia, "Candidatus Rickettsia andeanae." First identified in Peru, and subsequently reported in ticks collected in the United States, Chile, and Argentina, "Ca. R. andeanae" remains largely uncharacterized, in part because of the lack of a stable isolate. Although the isolation of "Ca. R. andeanae" was recently described in DH82, Vero, and Drosophila S2 cells, its stability in these cell lines was not shown. To evaluate "Ca. R. andeanae" transmission and pathogenicity in vertebrates, as well as further describe biological characteristics of this candidate species to fulfill criteria for its establishment as a new species, availability of a stable isolate is essential. Here we describe the propagation of "Ca. R. andeanae" by using a primary culture derived from naturally infected A. maculatum embryos. Subsequent passage of the "Ca. R. andeanae" isolate to ISE6 (Ixodes scapularis embryonic) and Vero (African green monkey kidney epithelial) cell lines demonstrated limited propagation of the rickettsiae. Treatment of the infected primary cells with tetracycline resulted in cultures negative for "Ca. R. andeanae" by polymerase chain reaction and microscopy. Establishment of an isolate of "Ca. R. andeanae" will promote further investigation into the significance of this tick-associated rickettsia, including its role in spotted fever and interactions with the sympatric species, R. parkeri in A.

A maize line resistant to herbivory constitutively releases (E) -beta-caryophyllene.

Various pests, such as those in the order Lepidoptera, frequently feed on young maize (Zea mays) plants and pose a significant threat to plant development and survival. To manage this problem, maize generates a wide variety of responses to attack by pests, from activation of wound-response pathways to the release of volatile compounds. Mp708, an inbred line resistant to feeding by the larvae of the fall armyworm (Spodoptera frugiperda J.E. Smith Lepidoptera: Noctuidae), has been developed through traditional breeding methods, but its underlying mechanisms of resistance are still not completely understood. Mp708 has been shown to have a moderately high constitutive expression of jasmonic acid (JA) before infestation by fall armyworm. However, Tx601, a genotype susceptible to feeding by fall armyworm, activates JA pathway only in response to feeding, suggesting that Mp708 is "primed" to respond swiftly to an attack. Current research indicates that fall armyworm show a lack of preference to feeding on Mp708, leading to the hypothesis that volatiles constitutively released by the plant may also play an important role in its resistance. Analysis of volatiles released by Mp708 and Tx601 in the presence and absence of fall armyworm larvae identified (E)-beta-caryophyllene, a terpenoid associated with resistance, released constitutively in Mp708. Fall armyworm fed samples of both Mp708 and Tx601 showed high transcript number of tps23, the gene responsible for the synthesis of (E)-beta-caryophyllene. In addition, fall armyworm larvae show a preference for Tx601 whorl tissue over Mp708 tissue, and the dosage of Tx601 whorl with (E)-beta-caryophyllene repels the fall armyworm.

The evolution of cranial form and function in theropod dinosaurs: insights from geometric morphometrics.

Theropod dinosaurs, an iconic clade of fossil species including Tyrannosaurus and Velociraptor, developed a great diversity of body size, skull form and feeding habits over their 160+ million year evolutionary history. Here, we utilize geometric morphometrics to study broad patterns in theropod skull shape variation and compare the distribution of taxa in cranial morphospace (form) to both phylogeny and quantitative metrics of biting behaviour (function). We find that theropod skulls primarily differ in relative anteroposterior length and snout depth and to a lesser extent in orbit size and depth of the cheek region, and oviraptorosaurs deviate most strongly from the "typical" and ancestral theropod morphologies. Noncarnivorous taxa generally fall out in distinct regions of morphospace and exhibit greater overall disparity than carnivorous taxa, whereas large-bodied carnivores independently converge on the same region of morphospace. The distribution of taxa in morphospace is strongly correlated with phylogeny but only weakly correlated with functional biting behaviour. These results imply that phylogeny, not biting function, was the major determinant of theropod skull shape.

The foot of Homo floresiensis.

Homo floresiensis is an endemic hominin species that occupied Liang Bua, a limestone cave on Flores in eastern Indonesia, during the Late Pleistocene epoch. The skeleton of the type specimen (LB1) of H. floresiensis includes a relatively complete left foot and parts of the right foot. These feet provide insights into the evolution of bipedalism and, together with the rest of the skeleton, have implications for hominin dispersal events into Asia. Here we show that LB1's foot is exceptionally long relative to the femur and tibia, proportions never before documented in hominins but seen in some African apes. Although the metatarsal robusticity sequence is human-like and the hallux is fully adducted, other intrinsic proportions and pedal features are more ape-like. The postcranial anatomy of H. floresiensis is that of a biped, but the unique lower-limb proportions and surprising combination of derived and primitive pedal morphologies suggest kinematic and biomechanical differences from modern human gait. Therefore, LB1 offers the most complete glimpse of a bipedal hominin foot that lacks the full suite of derived features characteristic of modern humans and whose mosaic design may be primitive for the genus Homo. These new findings raise the possibility that the ancestor of H. floresiensis was not Homo erectus but instead some other, more primitive, hominin whose dispersal into southeast Asia is still undocumented.

Practical understanding and use of surface enhanced Raman scattering/surface enhanced resonance Raman scattering in chemical and biological analysis.

The unique ability to obtain molecular recognition of an analyte at very low concentrations in situ in aqueous environments using surface enhanced Raman scattering (SERS) and surface enhanced resonance Raman scattering (SERRS) detection makes these spectroscopies of considerable interest. Improved understanding of the effect coupled to improvements in practical techniques make the use of SERS/SERRS much simpler than has been the case in the past. This article is designed as a tutorial review targeted at aiding in the development of practical applications.

Quantitative surface-enhanced resonance Raman scattering of phthalocyanine-labelled oligonucleotides.

The evaluation of phthalocyanine labels for the surface-enhanced resonance Raman scattering (SERRS) detection of oligonucleotides is reported. Three phthalocyanine-labelled oligonucleotides were assessed, each containing a different metal centre. Detection limits for each labelled oligonucleotide were determined using two excitation frequencies where possible. Limits of detection as low as 2.8 x 10(-11) mol. dm(-3) were obtained which are comparable to standard fluorescently labelled probes used in previous SERRS studies. The identification of two phthalocyanine-labelled oligonucleotides without separation was also demonstrated indicating their suitability for multiplexing. This study extends the range of labels suitable for quantitative surface-enhanced resonance Raman scattering with silver nanoparticles and offers more flexibility and choice when considering SERRS for quantitative DNA detection.

Practical control of SERRS enhancement.

The demonstration that quantitative and sensitive analysis can be carried out using surface enhanced resonance Raman scattering (SERRS) prompted a discussion and investigation of the main variables which are within the control of the analyst using colloidal silver as the substrate. Previous papers have dealt with the crucial need to obtain good chemisorption of the analyte to the surface and have reported the use of specially designed dyes for SERRS. One of the most variable processes is the aggregation of the colloid. Here, we investigate the addition of controlled amounts of an organic aggregating agent, poly-L-lysine, at concentrations which reduce the zeta potential in a controlled manner, thus aiding aggregation control. The relationship between the excitation frequency, the surface plasmon resonance frequency of the silver colloid and the frequency of the maximum absorbance of the molecular chromophore is studied using low concentrations of dye and no aggregating agent. Under these conditions, little to no aggregation is expected. The magnitude of the enhancement is strongly dependent on the frequency of the molecular chromophore as well as the plasmon resonance frequency. However, when sodium chloride is used to aggregate the colloid, a larger enhancement is obtained and the strong dependence on the molecular chromophore largely disappears. A much broader enhancement profile is obtained which appears to be related more to the specific enhancement processes caused by aggregation than the frequency of the chromophore. However, the total enhancement for SERRS is higher than for SERS thus indicating that the chromophore is still important to the process.

Three-dimensional optical trapping of partially silvered silica microparticles.

We demonstrate three-dimensional trapping of micrometer-diameter silica particles, partially coated with silver, within conventional optical tweezers. Although metallic particles are usually repelled from the beam focus by the scattering force, we show that transparent spheres partially coated with silver can be trapped with efficiencies comparable with dielectric particles. The trapping characteristics of these particles are examined as a function of metallic coverage, and the application of these particles to surface-enhanced resonance Raman scattering is investigated.

Fossils, feet and the evolution of human bipedal locomotion.

We review the evolution of human bipedal locomotion with a particular emphasis on the evolution of the foot. We begin in the early twentieth century and focus particularly on hypotheses of an ape-like ancestor for humans and human bipedal locomotion put forward by a succession of Gregory, Keith, Morton and Schultz. We give consideration to Morton's (1935) synthesis of foot evolution, in which he argues that the foot of the common ancestor of modern humans and the African apes would be intermediate between the foot of Pan and Hylobates whereas the foot of a hypothetical early hominin would be intermediate between that of a gorilla and a modern human. From this base rooted in comparative anatomy of living primates we trace changing ideas about the evolution of human bipedalism as increasing amounts of postcranial fossil material were discovered. Attention is given to the work of John Napier and John Robinson who were pioneers in the interpretation of Plio-Pleistocene hominin skeletons in the 1960s. This is the period when the wealth of evidence from the southern African australopithecine sites was beginning to be appreciated and Olduvai Gorge was revealing its first evidence for Homo habilis. In more recent years, the discovery of the Laetoli footprint trail, the AL 288-1 (A. afarensis) skeleton, the wealth of postcranial material from Koobi Fora, the Nariokotome Homo ergaster skeleton, Little Foot (Stw 573) from Sterkfontein in South Africa, and more recently tantalizing material assigned to the new and very early taxa Orrorin tugenensis, Ardipithecus ramidus and Sahelanthropus tchadensis has fuelled debate and speculation. The varying interpretations based on this material, together with changing theoretical insights and analytical approaches, is discussed and assessed in the context of new three-dimensional morphometric analyses of australopithecine and Homo foot bones, suggesting that there may have been greater diversity in human bipedalism in the earlier phases of our evolutionary history than previously suspected.

Characterization of novel Ag on TiO2 films for surface-enhanced Raman scattering.

Novel Ag on TiO2 films are generated by semiconductor photocatalysis and characterized by ultraviolet-visible (UV/Vis) spectroscopy, scanning electron microscopy (SEM), and atomic force microscopy (AFM), as well as assessed for surface-enhanced Raman scattering (SERS) activity. The nature and thickness of the photodeposited Ag, and thus the degree of SERS activity, is controlled by the time of exposure of the TiO2 film to UV light. All such films exhibit the optical characteristics (lambda(max) congruent with 390 nm) of small (< 20 nm) Ag particles, although this feature becomes less prominent as the film becomes thicker. The films comprise quite large (> 40 nm) Ag islands that grow and merge with increasing levels of Ag photodeposition. Tested with a benzotriazole dye probe, the films are SERS active, exhibiting activity similar to that of 6-nm-thick vapor-deposited films. The Ag/TiO2 films exhibit a lower residual standard deviation (approximately 25%) compared with Ag vapor-deposited films (approximately 45%), which is, however, still unacceptable for quantitative work. The sample-to-sample variance could be reduced significantly (< 7%) by spinning the film during the SERS measurement. The Ag/TiO2 films are mechanically robust and resistant to removal and damage by scratching, unlike the Ag vapor-deposited films. The Ag/TiO2 films also exhibit no obvious loss of SERS activity when stored in the dark under otherwise ambient conditions. The possible extension of this simple, effective method of producing Ag films for SERS, to metals other than Ag and to semiconductors other than TiO2, is briefly discussed.