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.

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

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.

Effects of dissolved oxygen availability and culture biomass at induction upon the intracellular expression of monoamine oxidase by recombinant E. coli in fed batch bioprocesses

The effects of oxygen availability and induction culture biomass upon production of an industrially important monoamine oxidase (MAO) were investigated in fed-batch cultures of a recombinant E. coli. For each induction cell biomass 2 different oxygenation methods were used, aeration and oxygen enriched air. Induction at higher biomass levels increased the culture demand for oxygen, leading to fermentative metabolism and accumulation of high levels of acetate in the aerated cultures. Paradoxically, despite an almost eight fold increase in acetate accumulation to levels widely reported to be highly detrimental to protein production, when induction wet cell weight (WCW) rose from 100% to 137.5%, MAO specific activity in these aerated processes showed a 3 fold increase. By contrast, for oxygenated cultures induced at WCW's 100% and 137.5% specific activity levels were broadly similar, but fell rapidly after the maxima were reached. Induction at high biomass levels (WCW 175%) led to very low levels of specific MAO activity relative to induction at lower WCW's in both aerated and oxygenated cultures. Oxygen enrichment of these cultures was a useful strategy for boosting specific growth rates, but did not have positive effects upon specific enzyme activity. Based upon our findings, consideration of the amino acid composition of MAO and previous studies on related enzymes, we propose that this effect is due to oxidative damage to the MAO enzyme itself during these highly aerobic processes. Thus, the optimal process for MAO production is aerated, not oxygenated, and induced at moderate cell density, and clearly represents a compromise between oxygen supply effects on specific growth rate/induction cell density, acetate accumulation, and high specific MAO activity. This work shows that the negative effects of oxygen previously reported in free enzyme preparations, are not limited to these acellular environments but are also discernible in the sheltered environment of the cytosol of E. coli cells.

Molecular structural studies of the amorphous mineral pitticite Fe, AsO4, SO4, H2O

Some minerals are colloidal and show no X-ray diffraction patterns. Vibrational spectroscopy offers one of the few methods for the assessment of the structure of these types of mineral. Among this group of minerals is pitticite simply described as Fe, AsO4, SO4, H2O. The objective of this research is to determine the molecular structure of the mineral pitticite using vibrational spectroscopy. Raman microscopy offers a useful method for the analysis of such colloidal minerals. Raman and infrared bands are attributed to the , and water stretching vibrations. The Raman spectrum is dominated by a very intense sharp band at 983 cm−1 assigned to the symmetric stretching mode. A strong Raman band at 1041 cm−1 is observed and is assigned to the antisymmetric stretching mode. Low intensity Raman bands at 757 and 808 cm−1 may be assigned to the antisymmetric and symmetric stretching modes. Raman bands observed at 432 and 465 cm−1 are attributable to the doubly degenerate ν2(SO4)2- bending mode.

Superoxide does react with peroxides : direct observation of the haber-weiss reaction in the gas phase

The fact that nature provides specific enzymes to selectively remove superoxide (O2.−) from aerobic organisms, namely, the superoxide dismutase enzymes,1 has led to the suggestion that this radical ion may cause the oxidative damage associated with degradative disease and aging.2 Intriguingly, however, superoxide itself is relatively unreactive toward most cellular components, which suggests that dismutase enzymes may ultimately protect the cell against more pernicious oxidants formed from superoxide. As such, there is increasing interest in the endogenous chemistry of superoxide and the pathways by which it might beget more reactive oxygen species. Protonation of superoxide to form the hydroperoxyl radical (HOO.) and dismutation of the same species to hydrogen peroxide (HOOH), with subsequent metal-catalyzed reduction to the hydroxyl radical (HO.), are well-characterized processes in which both the HOO. and HO. radicals are significantly more reactive than their common progenitor.2 Recent examples, however, have also linked superoxide to the putative production of singlet oxygen3 and ozone,4, 5 although the definitive characterization of these chemistries in the cellular milieu has proved challenging

The lowest singlet and triplet states of the oxyallyl diradical

Small S-T splitting : The photoelectron spectrum of the oxyallyl radical anion (see picture) reveals that the electronic ground state of oxyallyl is singlet, and the lowest triplet state is separated from the singlet state by only (55 ± 2) meV in adiabatic energy.

A molecular phylogeny of the checkered beetles and a description of Epiclininae a new subfamily (Coleoptera: Cleroidea: Cleridae)

We provide the first molecular phylogeny of the clerid lineage (Coleoptera: Cleridae, Thanerocleridae) within the superfamily Cleroidea to examine the two most recently-proposed hypotheses of higher-level classification. Phylogenetic relationships of checkered beetles were inferred from approximately ~5,000nt of both nuclear and mitochondrial rDNA (28S, 16S, and 12S) and the mitochondrial protein-coding gene COI. A worldwide sample of ~70 genera representing almost a quarter of generic diversity of the clerid lineage was included and phylogenies were reconstructed using Bayesian and Maximum Likelihood approaches. Results support the monophyly of many proposed subfamilies but were not entirely congruent with either current classification system. The subfamilial relationships within the Cleridae are resolved with support for three main lineages. Tillinae are supported as the sister group to all other subfamilies within the Cleridae, whereas Thaneroclerinae, Korynetinae and a new subfamily formally described here, Epiclininae subf. n, form a sister group to Clerinae + Hydnocerinae.

Molecular and structural basis of androgen receptor responses to dihydrotestosterone, medroxyprogesterone acetate and Δ4-tibolone

Medroxyprogesterone acetate (MPA) has widely been used in hormone replacement therapy (HRT), and is associated with an increased risk of breast cancer, possibly due to disruption of androgen receptor (AR) signaling. In contrast, the synthetic HRT Tibolone does not increase breast density, and is rapidly metabolized to estrogenic 3α-OH-tibolone and 3β-OH-tibolone, and a delta-4 isomer (Δ4-TIB) that has both androgenic and progestagenic properties. Here, we show that 5α-dihydrotestosterone (DHT) and Δ4-TIB, but not MPA, stabilize AR protein levels, initiate specific AR intramolecular interactions critical for AR transcriptional regulation, and increase proliferation of AR positive MDA-MB-453 breast cancer cells. Structural modeling and molecular dynamic simulation indicate that Δ4-TIB induces a more stable AR structure than does DHT, and MPA a less stable one. Microarray expression analyses confirms that the molecular actions of Δ4-TIB more closely resembles DHT in breast cancer cells than either ligand does to MPA.

Exercise alters the profile of phospholipid molecular species in rat skeletal muscle

We have determined the effect of two exercise-training intensities on the phospholipid profile of both glycolytic and oxidative muscle fibers of female Sprague-Dawley rats using electrospray-ionization mass spectrometry. Animals were randomly divided into three training groups: control, which performed no exercise training; low-intensity (8 m/min) treadmill running; or high-intensity (28 m/min) treadmill running. All exercise-trained rats ran 1,000 m/session for 4 days/wk for 4 wk and were killed 48 h after the last training bout. Exercise training was found to produce no novel phospholipid species but was associated with significant alterations in the relative abundance of a number of phospholipid molecular species. These changes were more prominent in glycolytic (white vastus lateralis) than in oxidative (red vastus lateralis) muscle fibers. The largest observed change was a decrease of ∼20% in the abundance of 1-stearoyl-2-docosahexaenoyl-phosphatidylethanolamine [PE(18:0/22:6); P < 0.001] ions in both the low- and high-intensity training regimes in glycolytic fibers. Increases in the abundance of 1-oleoyl-2-linoleoyl phopshatidic acid [PA(18:1/18:2); P < 0.001] and 1-alkenylpalmitoyl-2-linoleoyl phosphatidylethanolamine [plasmenyl PE (16:0/18:2); P < 0.005] ions were also observed for both training regimes in glycolytic fibers. We conclude that exercise training results in a remodeling of phospholipids in rat skeletal muscle. Even though little is known about the physiological or pathophysiological role of specific phospholipid molecular species in skeletal muscle, it is likely that this remodeling will have an impact on a range of cellular functions.

Photoelectron spectroscopy of HCCN- and HCNC- reveals the quasilinear triplet carbenes, HCCN and HCNC

Negative ion photoelectron spectroscopy has been used to study the HCCN- and HCNC- ions. The electron affinities (EA) of cyanocarbene have been measured to be EA(HCCN (X) over tilde (3)Sigma(-)=2.003+/-0.014 eV and EA(DCCN (X) over tilde (3)Sigma(-))=2.009+/-0.020 eV. Photodetachment of HCCN- to HCCN (X) over tilde (3)Sigma(-) shows a 0.4 eV long vibrational progression in nu(5), the H-CCN bending mode; the HCCN- photoelectron spectra reveal excitations up to 10 quanta in nu(5). The term energies for the excited singlet state are found to be T-0(HCCN (a) over tilde (1)A('))=0.515+/-0.016 eV and T-0(DCCN (a) over tilde (1)A('))=0.518+/-0.027 eV. For the isocyanocarbene, the two lowest states switch and HCNC has a singlet ground state and an excited triplet state. The electron affinities are EA(HCNC (X) over tilde (1)A('))=1.883+/-0.013 eV and EA((X) over tilde (1)A(') DCNC)=1.877+/-0.010 eV. The term energy for the excited triplet state is T-0(HCNC (a) over tilde (3)A("))=0.050+/-0.028 eV and T-0(DCNC (a) over tilde (3)A("))=0.063+/-0.030 eV. Proton transfer kinetics in a flowing afterglow apparatus were used to re-measure the enthalpy of deprotonation of CH3NC to be Delta(acid)H(298)(CH3NC)=383.6+/-0.6 kcal mol(-1). The acidity/EA thermodynamic cycle was used to deduce D-0(H-CHCN)=104+/-2 kcal mol(-1) [Delta(f)H(0)(HCCN)=110+/-4 kcal mol(-1)] and D-0(H-CHNC)=106+/-4 kcal mol(-1) [Delta(f)H(0)(HCNC)=133+/-5 kcal mol(-1)]. (C) 2002 American Institute of Physics.