Structures of life : the role of molecular structures in scientists' work

The visual and multidimensional representations like images and graphical structures related to biology provide great insights into understanding the complexities of different organisms. Especially, life scientists use different representations of molecular structures to answer biological questions and to better understand cellular processes. Combining results from two field studies, we explore the role of molecular structures in life scientists’ current work from a humanfactors perspective. Our main conclusion is that different representations of molecular structures, due to their visual nature, are important for supporting collaboration, constructing new knowledge and supporting scientists’ professional activities in general.

Accurate measurement of the molecular thickness of thin organic shells on small inorganic cores using dynamic light scattering

Dynamic light scattering (DLS) has become a primary nanoparticle characterization technique with applications from materials characterization to biological and environmental detection. With the expansion in DLS use from homogeneous spheres to more complicated nanostructures, comes a decrease in accuracy. Much research has been performed to develop different diffusion models that account for the vastly different structures but little attention has been given to the effect on the light scattering properties in relation to DLS. In this work, small (core size < 5 nm) core-shell nanoparticles were used as a case study to measure the capping thickness of a layer of dodecanethiol (DDT) on Au and ZnO nanoparticles by DLS. We find that the DDT shell has very little effect on the scattering properties of the inorganic core and hence can be ignored to a first approximation. However, this results in conventional DLS analysis overestimating the hydrodynamic size in the volume and number weighted distributions. By introducing a simple correction formula that more accurately yields hydrodynamic size distributions a more precise determination of the molecular shell thickness is obtained. With this correction, the measured thickness of the DDT shell was found to be 7.3 ± 0.3 Å, much less than the extended chain length of 16 Å. This organic layer thickness suggests that on small nanoparticles, the DDT monolayer adopts a compact disordered structure rather than an open ordered structure on both ZnO and Au nanoparticle surfaces. These observations are in agreement with published molecular dynamics results.

The molecular structure of the vanadate mineral mottramite [PbCu(VO4)(OH)] from Tsumeb, Namibia – a vibrational spectroscopic study

We have studied a mineral sample of mottramite PbCu(VO4)(OH) from Tsumeb, Namibia using a combination of scanning electron microscopy with EDX, Raman and infrared spectroscopy. Chemical analysis shows principally the elements V, Pb and Cu. Ca occurs as partial substitution of Pb as well as P and As in substitution to V. Minor amounts of Si and Cr were also observed. The Raman band of mottramite at 829 cm-1, is assigned to the ν1 symmetric (VO-4) ) stretching mode. The complexity of the spectra is attributed to the chemical composition of the Tsumeb mottramite. The ν3 antisymmetric vibrational mode of mottramite is observed as very low intensity bands at 716 and 747 cm-1. The series of Raman bands at 411, 439, 451 cm-1 and probably also the band at 500 cm-1 are assigned to the (VO-4) ν2 bending mode. The series of Raman bands at 293, 333 and 366 cm-1 are attributed to the (VO-4) ) ν4 bending modes. The ν3, ν3 and ν4 regions are complex for both minerals and this is attributed to symmetry reduction of the vanadate unit from Td to Cs.

The molecular structure of the borate mineral rhodizite (K, Cs)Al4Be4(B, Be)12O28 – A vibrational spectroscopic study

We have studied the borate mineral rhodizite (K, Cs)Al4Be4(B, Be)12O28 using a combination of DEM with EDX and vibrational spectroscopic techniques. The mineral occurs as colorless, gray, yellow to white crystals in the triclinic crystal system. The studied sample is from the Antandrokomby Mine, Sahatany valley, Madagascar. The mineral is prized as a semi-precious jewel. Semi-quantitative chemical composition shows a Al, Ca, borate with minor amounts of K, Mg and Cs. The mineral has a characteristic borate Raman spectrum and bands are assigned to the stretching and bending modes of B, Be and Al. No Raman bands in the OH stretching region were observed.

The molecular structure of the phosphate mineral beraunite Fe2+Fe⅗+(PO4)4(OH)5⋅4H2O– A vibrational spectroscopic study

The mineral beraunite from Boca Rica pegmatite in Minas Gerais with theoretical formula Fe2+Fe5 3+(PO4)4(OH)5⋅4H2O has been studied using a combination of electron microscopy with EDX and vibrational spectroscopic techniques. Raman spectroscopy identifies an intense band at 990 cm-1 and 1011 cm-1. These bands are attributed to the PO4 3- v, symmetric stretching mode. The m3 antisymmetric stretching modes are observed by a large number of Raman bands. The Raman bands at 1034, 1051, 1058, 1069 and 1084 together with the Raman bands at 1098, 1116, 1133, 1155 and 1174 cm-1 are assigned to the m3 antisymmetric stretching vibrations of PO4 3- and the HOPO3 2- units. The observation of these multiple Raman bands in the symmetric and antisymmetric stretching region gives credence to the concept that both phosphate and hydrogen phosphate units exist in the structure of beraunite. The series of Raman bands at 567, 582,601, 644, 661, 673, and 687 cm-1 are assigned to the PO4 3- v2 bending modes. The series of Raman bands at 437, 468, 478, 491, 503 cm-1 are attributed to the PO4 3- and OPO3 2- v4 bending modes. No Raman bands of beraunite which could be attributed to the hydroxyl stretching unit were observed. Infrared bands at 3511 and 3359 cm-1 are ascribed to the OH stretching vibration of the OH units. Very broad bands at 3022 and 3299 cm-1 are attributed to the OH stretching vibrations of water. Vibrational spectroscopy offers insights into the molecular structure of the phosphate mineral beraunite.

Impacts of climatic factors on evolution of molecular diversity and the natural distribution of wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii)

Natural distributions of most freshwater taxa are restricted geographically, a pattern that reflects dispersal limitation. Macrobrachium rosenbergii is unusual because it occurs naturally in rivers from near Pakistan in the west, across India and Bangladesh to the Malay Peninsula, and across the Sunda Shelf and Indonesian archipelago to western Java. Individuals cannot tolerate full marine conditions, so dispersal between river drainage basins must occur at limited geographical scales when ecological or climatic factors are favorable. We examined molecular diversity in wild populations of M. rosenbergii across its complete natural range to document patterns of diversity and to relate them to factors that have driven evolution of diversity in this species. We found 3 clades in the mitochondrial deoxyribonucleic acid (mtDNA) data set that corresponded geographically with eastern, central, and western sets of haplotypes that last shared a common ancestor 1 × 106 y ago. The eastern clade was closest to the common ancestor of all 3 clades and to the common ancestor with its congener, Macrobrachium spinipes, distributed east of Huxley's Line. Macrobrachium rosenbergii could have evolved in the western Indonesian archipelago and spread westward during the early to mid-Pleistocene to India and Sri Lanka. Additional groups identified in the nuclear DNA data set in the central and western clades probably indicate secondary contact via dispersal between regions and modern introductions that have mixed nuclear and mtDNA genes. Pleistocene sea-level fluctuations can explain dispersal across the Indonesian archipelago and parts of mainland southeastern Asia via changing river drainage connections in shallow seas on wide continental shelves. At the western end of the modern distribution where continental shelves are smaller, intermittent freshwater plumes from large rivers probably permitted larval dispersal across inshore areas of lowered salinity.

Molecular dynamics simulation of mechanical behavior of osteopontin-hydroxyapatite interfaces

Bone is characterized with an optimized combination of high stiffness and toughness. The understanding of bone nanomechanics is critical to the development of new artificial biological materials with unique properties. In this work, the mechanical characteristics of the interfaces between osteopontin (OPN, a noncollagenous protein in extrafibrillar protein matrix) and hydroxyapatite (HA, a mineral nanoplatelet in mineralized collagen fibrils) were investigated using molecular dynamics method. We found that the interfacial mechanical behaviour is governed by the electrostatic attraction between acidic amino acid residues in OPN and calcium in HA. Higher energy dissipation is associated with the OPN peptides with a higher number of acidic amino acid residues. When loading in the interface direction, new bonds between some acidic residues and HA surface are formed, resulting in a stick-slip type motion of OPN peptide on the HA surface and high interfacial energy dissipation. The formation of new bonds during loading is considered to be a key mechanism responsible for high fracture resistance observed in bone and other biological materials.

Bauxite residue neutralisation precipitate stability in acidic environments

This investigation used a combination of techniques, such as X-ray diffraction, inductively coupled plasma optical emission spectroscopy and infrared spectroscopy, to determine the dissolution mechanisms of the Bayer precipitate and the associated rate of dissolution in acetic, citric and oxalic acid environments. The Bayer precipitate is a mixture of hydrotalcite, calcium carbonate and sodium chloride that forms during the seawater neutralisation of Bayer liquors (waste residue of the alumina industry). The dissolution rate of a Bayer precipitate is found to be dependent on (1) the strength of the organic acid and (2) the number of donating H+ ions. The dissolution mechanism for a Bayer precipitate consists of several steps involving: (1) the dissolution of CaCO3, (2) formation of whewellite (calcium oxalate) when oxalic acid is used and (3) multiple dissolution steps for hydrotalcite that are highly dependent on the pH of solution. The decomposition of the Al–OH hydrotalcite layers resulted in the immediate formation of Al(OH)3, which is stable until the pH decreases below 5.5. This investigation has found that the Bayer precipitate is stable across a wide pH range in the presence of common organic acids found in the rhizosphere, and that initial decomposition steps are likely to be beneficial in supporting plant growth through the release of nutrients such as Ca2þ and Mg2þ.

Vibrational spectroscopic characterization of the sulphate mineral leightonite K2Ca2Cu(SO4)4⋅2H2O – Implications for the molecular structure

The mineral leightonite, a rare sulphate mineral of formula K2Ca2Cu(SO4)4.2H2O, has been studied using a combination of electron probe and vibrational spectroscopy. The mineral is characterized by an intense Raman band at 991 cm-1 attributed to the SO2- 4 m1 symmetric stretching mode. A series of Raman bands at 1047, 1120, 1137, 1163 and 1177 cm-1 assigned to the SO2- 4 m3 antisymmetric stretching modes. The observation of multiple bands shows that the symmetry of the sulphate anion is reduced. Multiple Raman and infrared bands in the OH stretching region shows that water in the structure of leightonite is in a range of molecular environments.

Epidemiological and molecular features of dengue virus type-1 in New Caledonia, South Pacific, 2001–2013

Background The epidemiology of dengue in the South Pacific has been characterized by transmission of a single dominant serotype for 3–5 years, with subsequent replacement by another serotype. From 2001 to 2008 only DENV-1 was reported in the Pacific. In 2008, DENV-4 emerged and quickly displaced DENV-1 in the Pacific, except in New Caledonia (NC) where DENV-1 and DENV-4 co-circulated in 2008–2009. During 2012–2013, another DENV-1 outbreak occurred in NC, the third DENV-1 outbreak in a decade. Given that dengue is a serotype-specific immunizing infection, the recurrent outbreaks of a single serotype within a 10-year period was unexpected. Findings This study aimed to inform this phenomenon by examining the phylogenetic characteristics of the DENV-1 viruses in NC and other Pacific islands between 2001 and 2013. As a result, we have demonstrated that NC experienced introductions of viruses from both the Pacific (genotype IV) and South-east Asia (genotype I). Moreover, whereas genotype IV and I were co-circulating at the beginning of 2012, we observed that from the second half of 2012, i.e. during the major DENV-1 outbreak, all analyzed viruses were genotype I suggesting that a genotype switch occurred. Conclusions Repeated outbreaks of the same dengue serotype, as observed in NC, is uncommon in the Pacific islands. Why the earlier DENV-1 outbreaks did not induce sufficient herd immunity is unclear, and likely multifactorial, but the robust vector control program may have played a role by limiting transmission and thus maintaining a large susceptible pool in the population. Keywords: Dengue; Phylogeny; Genotype; Epidemics; New Caledonia

IT governance stability in a political changing environment : exploring potential impacts in the public sector

Public sector organisations (PSOs) operate in information-intensive environments often within operational contexts where efficiency is a goal. What's more, the rapid adoption of IT is expected to facilitate good governance within public sector organisations but it often clashes with the bureaucratic culture of these organisations. Accordingly, models such as IT Governance (ITG) and government reform -in particular the new public management (NPM)- were introduced in PSOs in an effort to address the inefficiencies of bureaucracy and under performance. This work explores the potential effect of change in political direction and policy on the stability of IT governance in Australian public sector organisations. The aim of this paper is to examine implications of a change of government and the resulting political environment on the effectiveness of the audit function of ITG. The empirical data discussed here indicate that a number of aspects of audit functionality were negatively affected by change in political direction and resultant policy changes. The results indicate a perceived decline in capacity and capability which in turn disrupts the stability of IT governance systems in public sector organisations.

Supramolecular selection in molecular and framework co-crystals

An ongoing challenge in chemistry and crystal engineering is the synthesis of functional materials with predictable structures and customisable properties. This may be achieved by crystallising mixtures of different compounds. Co-crystals formed through this method have predictable structures and their properties may be tuned by varying the ratio of the compounds in the crystallising solution. This thesis examines single crystals formed by the co-crystallisation of metal complexes that have similar structures but different physical or chemical properties. A variety of new compounds with interesting properties were prepared, characterised and their significance in the context of crystal engineering was explored.

Stability of the bituminous coal microstructure upon exposure to high pressures of helium

Small-angle neutron scattering (SANS) and ultra-small-angle neutron scattering (USANS) measurements of the structure of two Australian bituminous coals (particle size of 1-0.5 mm) before, during, and after exposure to 155 bar of helium were made to identify any effects of pressure alone on the pore size distribution of coal and any irreversible effects upon exposure to high pressures of helium in the pore size range from 3 nm to 10 μm. No irreversible effects upon exposure were identified for any pore size. No effects of pressure on pore size distribution were observed, except for a small effect at a pore size of about 2 μm for one coal. This study provides a convenient baseline for SANS and USANS investigations on sorption of gases at elevated pressures on coals, by distinguishing between the effect of pressure alone on coal pore size distribution and against the effect of the gas to be investigated.

New criterion for the stability of a human body in floodwaters

The authors must be congratulated for their original and important study. The flooding of urbanised areas constitutes a hazard to the population and infrastructure. Floods through inundated urban environments have been studied only recently and few considered the potential impact of flowing waters on pedestrians...