Vibrational spectroscopy of the borate mineral tunellite SrB6O9(OH)2·3(H2O) : implications for the molecular structure

Tunellite is a strontium borate mineral with formula: SrB6O9(OH)2∙3(H2O) and occurs as colorless crystals in the monoclinic pyramidal crystal system. An intense Raman band at 994 cm-1 was assigned to the BO stretching vibration of the B2O3 units. Raman bands at 1043, 1063, 1082 and 1113 cm-1 are attributed to the in-plane bending vibrations of trigonal boron. Sharp Raman bands observed at 464, 480, 523, 568 and 639 cm-1 are simply defined as trigonal and tetrahedral borate bending modes. The Raman spectrum clearly shows intense Raman bands at 3567 and 3614 cm-1, attributed to OH units. The molecular structure of a natural tunellite has been assessed by using vibrational spectroscopy.

The RNA world in plants: Post-transcriptional control III

Post-transcriptional control of gene expression has gone from a curiosity involving a few special genes to a highly diverse and widespread set of processes that is truly pervasive in plant gene expression. Thus, Plant Cell readers interested in almost any aspect of plant gene expression in response to any environmental influence, or in development, are advised to read on. In May 2001, what has become the de facto third biennial Symposium on Post-Transcriptional Control of Gene Expression in Plants was held in Ames, Iowa. The meeting was hosted by the new Plant Sciences Institute of Iowa State University with additional funding from the National Science Foundation and the United States Department of Agriculture. In 1997, the annual University of California-Riverside Plant Physiology Symposium was devoted to this topic. This provided a wake-up call to the plant world, summarized in this journal (Gallie and Bailey-Serres, 1997), that not all gene expression is controlled at the level of transcription. This was expanded upon at a European Molecular Biology Organization Workshop in Leysin, Switzerland, in 1999 (Bailey-Serres et al., 1999). The 3-day meeting in Ames brought together a strong and diverse contingent of plant biologists from four continents. The participants represented an unusually heterogeneous group of disciplines ranging from virology to stress response to computational biology. The research approaches and techniques represented were similarly diverse. Here we discuss a sample of the many fascinating aspects of post-transcriptional control that were presented at this meeting; we apologize to those whose work is not described here.

The use of artificial MicroRNA technology to control gene expression in Arabidopsis thaliana

In plants, double-stranded RNA (dsRNA) is an effective trigger of RNA silencing, and several classes of endogenous small RNA (sRNA), processed from dsRNA substrates by DICER-like (DCL) endonucleases, are essential in controlling gene expression. One such sRNA class, the microRNAs (miRNAs) control the expression of closely related genes to regulate all aspects of plant development, including the determination of leaf shape, leaf polarity, flowering time, and floral identity. A single miRNA sRNA silencing signal is processed from a long precursor transcript of nonprotein-coding RNA, termed the primary miRNA (pri-miRNA). A region of the pri-miRNA is partially self-complementary allowing the transcript to fold back onto itself to form a stem-loop structure of imperfectly dsRNA. Artificial miRNA (amiRNA) technology uses endogenous pri-miRNAs, in which the miRNA and miRNA*(passenger strand of the miRNA duplex) sequences have been replaced with corresponding amiRNA/ amiRNA*sequences that direct highly efficient RNA silencing of the targeted gene. Here, we describe the rules for amiRNA design, as well as outline the PCR and bacterial cloning procedures involved in the construction of an amiRNA plant expression vector to control target gene expression in Arabidopsis thaliana. © 2014 Springer Science+Business Media New York.

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.

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

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.

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.

Paracrine interactions between LNCaP prostate cancer cells and bioengineered bone in 3D in vitro culture reflect molecular changes during bone metastasis

As microenvironmental factors such as three-dimensionality and cell–matrix interactions are increasingly being acknowledged by cancer biologists, more complex 3D in vitro models are being developed to study tumorigenesis and cancer progression. To better understand the pathophysiology of bone metastasis, we have established and validated a 3D indirect co-culture model to investigate the paracrine interactions between prostate cancer (PCa) cells and human osteoblasts. Co-culture of the human PCa, LNCaP cells embedded within polyethylene glycol hydrogels with human osteoblasts in the form of a tissue engineered bone construct (TEB), resulted in reduced proliferation of LNCaP cells. LNCaP cells in both monoculture and co-culture were responsive to the androgen analog, R1881, as indicated by an increase in the expression (mRNA and/or protein induction) of androgen-regulated genes including prostate specific antigen and fatty acid synthase. Microarray gene expression analysis further revealed an up-regulation of bone markers and other genes associated with skeletal and vasculature development and a significant activation of transforming growth factor β1 downstream genes in LNCaP cells after co-culture with TEB. LNCaP cells co-cultured with TEB also unexpectedly showed similar changes in classical androgen-responsive genes under androgen-deprived conditions not seen in LNCaP monocultures. The molecular changes of LNCaP cells after co-culturing with TEBs suggest that osteoblasts exert a paracrine effect that may promote osteomimicry and modulate the expression of androgen-responsive genes in LNCaP cells. Taken together, we have presented a novel 3D in vitro model that allows the study of cellular and molecular changes occurring in PCa cells and osteoblasts that are relevant to metastatic colonization of bone. This unique in vitro model could also facilitate cancer biologists to dissect specific biological hypotheses via extensive genomic or proteomic assessments to further our understanding of the PCa-bone crosstalk.

Myoepithelial molecular markers in human breast carcinoma PMC42-LA cells are induced by extracellular matrix and stromal cells

The microenvironment plays a key role in the cellular differentiation of the two main cell lineages of the human breast, luminal epithelial, and myoepithelial. It is not clear, however, how the components of the microenvironment control the development of these cell lineages. To investigate how lineage development is regulated by 3-D culture and microenvironment components, we used the PMC42-LA human breast carcinoma cell line, which possesses stem cell characteristics. When cultured on a two-dimensional glass substrate, PMC42-LA cells formed a monolayer and expressed predominantly luminal epithelial markers, including cytokeratins 8, 18, and 19; E-cadherin; and sialomucin. The key myoepithelial-specific proteins α-smooth muscle actin and cytokeratin 14 were not expressed. When cultured within Engelbreth-Holm- Swarm sarcoma-derived basement membrane matrix (EHS matrix), PMC42-LA cells formed organoids in which the expression of luminal markers was reduced and the expression of other myoepithelial-specific markers (cytokeratin 17 and P-cadherin) was promoted. The presence of primary human mammary gland fibroblasts within the EHS matrix induced expression of the key myoepithelial-specific markers, α-smooth muscle actin and cytokeratin 14. Immortalized human skin fibroblasts were less effective in inducing expression of these key myoepithelial-specific markers. Confocal dual-labeling showed that individual cells expressed luminal or myoepithelial proteins, but not both. Conditioned medium from the mammary fibroblasts was equally effective in inducing myoepithelial marker expression. The results indicate that the myoepithelial lineage is promoted by the extracellular matrix, in conjunction with products secreted by breast-specific fibroblasts. Our results demonstrate a key role for the breast microenvironment in the regulation of breast lineage development.

Intercalation of dodecylamine into kaolinite and its layering structure investigated by molecular dynamics simulation

Dodecylamine was successfully intercalated into the layer space of kaolinite by utilizing the methanol treated kaolinite–dimethyl sulfoxide (DMSO) intercalation complex as an intermediate. The basal spacing of kaolinite, measured by X-ray diffraction (XRD), increased from 0.72 nm to 4.29 nm after the intercalation of dodecylamine. Also, the significant variation observed in the Fourier Transform Infrared Spectroscopy (FTIR) spectra of kaolinite when intercalated with dodecylamine verified the feasibility of intercalation of dodecylamine into kaolinite. Isothermal-isobaric (NPT) molecular dynamics simulation with the use of Dreiding force field was performed to probe into the layering behavior and structure of nanoconfined dodecylamine in the kaolinite gallery. The concentration profiles of the nitrogen atom, methyl group and methylene group of intercalated dodecylamine molecules in the direction perpendicular to the kaolinite basal surface indicated that the alkyl chains within the interlayer space of kaolinite exhibited an obvious layering structure. However, the unified bilayer, pseudo-trilayer, or paraffin-type arrangements of alkyl chains deduced based on their chain length combined with the measured basal spacing of organoclays were not found in this study. The alkyl chains aggregated to a mixture of ordered paraffin-type-like structure and disordered gauche conformation in the middle interlayer space of kaolinite, and some alkyl chains arranged in two bilayer structures, in which one was close to the silica tetrahedron surface, and the other was close to the alumina octahedron surface with their alkyl chains parallel to the kaolinite basal surface.

Proteins, drug targets and the mechanisms they control : the simple truth about complex networks

Realizing the promise of molecularly targeted inhibitors for cancer therapy will require a new level of knowledge about how a drug target is wired into the control circuitry of a complex cellular network. Here we review general homeostatic principles of cellular networks that enable the cell to be resilient in the face of molecular perturbations, while at the same time being sensitive to subtle input signals. Insights into such mechanisms may facilitate the development of combination therapies that take advantage of the cellular control circuitry, with the aim of achieving higher efficacy at a lower drug dosage and with a reduced probability of drug-resistance development.