Phylogeography and Adaptive Divergence of Three-spined Stickleback Populations

Genetic studies on phylogeography and adaptive divergence in Northern Hemisphere fish species such as three-spined stickleback (Gasterosteus aculeatus) provide an excellent opportunity to investigate genetic mechanisms underlying population differentiation. According to the theory, the process of population differentiation results from a complex interplay between random and deterministic processes as well historical factors. The main scope in this thesis was to study how historical factors like the Pleistocene ice ages have shaped the patterns molecular diversity in three-spined stickleback populations in Europe and how this information could be utilized in the conservation genetic context. Furthermore, identifying footprints of natural selection at the DNA level might be used in identifying genes involved in evolutionary change. Overall, the results from phylogeographic studies indicate that the three-spined stickleback has colonized the Atlantic basin relatively recently but constitutes three major evolutionary lineages in Europe. In addition, the colonization of freshwater appears to result from multiple and independent invasions by the marine conspecifics. Molecular data together with morphology suggest that the most divergent freshwater populations are located in the Balkan Peninsula and these populations deserve a special conservation genetic status without warranting further taxonomical classification. In order to investigate the adaptive divergence in Fennoscandian three-spined stickleback populations several approaches were used. First, sequence variability in the Eda-gene, coding for the number of lateral plates, was concordant with the previously observed global pattern. Full plated allele is in high frequencies among marine populations whereas low plated allele dominates in the freshwater populations. Second, a microsatellite based genome scan identified both indications of balancing and directional selection in the three-spined stickleback genome, i.e. loci with unusually similar or unusually different allele frequencies over populations. The directionally selected loci were mainly associated with the adaptation to freshwater. A follow up study conducting a more detailed analysis in a chromosome region containing a putatively selected gene locus identified a fairly large genomic region affected by natural selection. However, this region contained several gene predictions, all of which might be the actual target of natural selection. All in all, the phylogeographic and adaptive divergence studies indicate that most of the genetic divergence has occurred in the freshwater populations whereas the marine populations have remained relatively uniform.

The genome packaging machinery of dsDNA bacteriophage PRD1

Viral genomes are encapsidated within protective protein shells. This encapsidation can be achieved either by a co-condensation reaction of the nucleic acid and coat proteins, or by first forming empty viral particles which are subsequently packaged with nucleic acid, the latter mechanism being typical for many dsDNA bacteriophages. Bacteriophage PRD1 is an icosahedral, non-tailed dsDNA virus that has an internal lipid membrane, the hallmark of the Tectiviridae family. Although PRD1 has been known to assemble empty particles into which the genome is subsequently packaged, the mechanism for this has been unknown, and there has been no evidence for a separate packaging vertex, similar to the portal structures used for packaging in the tailed bacteriophages and herpesviruses. In this study, a unique DNA packaging vertex was identified for PRD1, containing the packaging ATPase P9, packaging factor P6 and two small membrane proteins, P20 and P22, extending the packaging vertex to the internal membrane. Lack of small membrane protein P20 was shown to totally abolish packaging, making it an essential part of the PRD1 packaging mechanism. The minor capsid proteins P6 was shown to be an important packaging factor, its absence leading to greatly reduced packaging efficiency. An in vitro DNA packaging mechanism consisting of recombinant packaging ATPase P9, empty procapsids and mutant PRD1 DNA with a LacZ-insert was developed for the analysis of PRD1 packaging, the first such system ever for a virus containing an internal membrane. A new tectiviral sequence, a linear plasmid called pBClin15, was identified in Bacillus cereus, providing material for sequence analysis of the tectiviruses. Analysis of PRD1 P9 and other putative tectiviral ATPase sequences revealed several conserved sequence motifs, among them a new tectiviral packaging ATPase motif. Mutagenesis studies on PRD1 P9 were used to confirm the significance of the motifs. P9-type putative ATPase sequences carrying a similar sequence motif were identified in several other membrane containing dsDNA viruses of bacterial, archaeal and eukaryotic hosts, suggesting that these viruses may have similar packaging mechanisms. Interestingly, almost the same set of viruses that were found to have similar putative packaging ATPases had earlier been found to share similar coat protein folds and capsid structures, and a common origin for these viruses had been suggested. The finding in this study of similar packaging proteins further supports the idea that these viruses are descendants of a common ancestor.

Stereochemistry of peptides and polypeptides containing omega amino acids

The omega amino acids have a larger degree of conformational variability than the alpha amino acids, leading to a greater diversity of backbone structures in peptides and polypeptides. The synthetic accessibility of chiral beta-amino acids and the recent observation of novel helical folds in oligomers of cyclic beta-amino acids has led to renewed interest in the stereochemistry of omega-amino acid containing peptides. This review focuses on the conformational characteristics of the polymethylene chain in omega-amino acid segments and surveys structural features in peptides established by X-ray diffraction. The literature on polymers of achiral omega-amino acids (nylon derivatives) and chiral, substituted derivatives derived from trifunctional alpha-amino acids, reveals that while sheet-like, intermolecular hydrogen bonded structures are formed by the former, folded helices appear favoured by the latter. omega-Amino acids promise to expand the repertoire of peptide folds.

Taxonomy and redescription of the Swamp Antechinus, Antechinus minimus (E. Geoffroy) (Marsupialia: Dasyuridae)

We provide a taxonomic redescription of the dasyurid marsupial Swamp Antechinus, Antechinus minimus (Geoffroy, 1803). In the past, A. minimus has been classified as two subspecies: the nominate A. minimus minimus (Geoffroy, 1803), which is found throughout much of Tasmania (including southern Bass Strait islands) and A. minimus maritimus (Finlayson, 1958), which is found on mainland Australia (as well as some near-coastal islands) and is patchily distributed in mostly coastal areas between South Gippsland (Victoria) and Robe (South Australia). Based on an assessment of morphology and DNA, we conclude that A. minimus is both distinctly different from all extant congeners and that the two existing subspecies of Swamp Antechinus are appropriately taxonomically characterised. In our genetic phylogenies, the Swamp Antechinus was monophyletic with respect to all 14 known extant congeners; moreover, A. minimus was well-positioned in a large clade, together with all four species in the Dusky Antechinus complex, to the exclusion of all other antechinus. Within A. minimus, between subspecies there were subtle morphological differences (A. m. maritimus skulls tend to be broader, with larger molar teeth, than A. m. minimus, but these differences were not significant); there was distinct, but only moderately deep genetic differences (3.9–4.5% at mtDNA) between A. minimus subspecies. Comparatively, across Bass Strait, the two subspecies of A. minimus are morphologically and genetically markedly less divergent than recently recognised species pairs within the Dusky Antechinus complex, found in Victoria (A. mimetes) and Tasmania (A. swainsonii) (9.4–11.6% divergent at mtDNA)

An investigation of first-order transition across charge ordered and ferromagnetic phases in Gd0.5Sr0.5MnO3 single crystals by magnetic and magnetotransport studies

Gadolinium strontium manganite single crystals of the composition Gd0.5Sr0.5MnO3 were grown using the optical float zone method. We report here the magnetic and magnetotransport properties of these crystals. A large magnetoresistance similar to 10(9)% was observed at 45 K under the application of a 110 kOe field. We have observed notable thermomagnetic anomalies such as open hysteresis loops across the broadened first-order transition between the charge order insulator and the ferromagnetic metallic phase while traversing the magnetic field-temperature (H-T) plane isothermally or isomagnetically. In order to discern the cause of these observed anomalies, the H-T phase diagram for Gd0.5Sr0.5MnO3 is formulated using the magnetization-field (M-H), magnetization-temperature (M-T) and resistance-temperature (R-T) measurements. The temperature dependence of the critical field (i.e. H-up, the field required for transformation to the ferromagnetic metallic phase) is non-monotonic. We note that the non-monotonic variation of the supercooling limit is anomalous according to the classical concepts of the first-order phase transition. Accordingly, H-up values below similar to 20 K are unsuitable to represent the supercooling limit. It is possible that the nature of the metastable states responsible for the observed open hysteresis loops is different from that of the supercooled ones.

Structure-Based Phylogeny as a Diagnostic for Functional Characterization of Proteins with a Cupin Fold

Background: The members of cupin superfamily exhibit large variations in their sequences, functions, organization of domains, quaternary associations and the nature of bound metal ion, despite having a conserved beta-barrel structural scaffold. Here, an attempt has been made to understand structure-function relationships among the members of this diverse superfamily and identify the principles governing functional diversity. The cupin superfamily also contains proteins for which the structures are available through world-wide structural genomics initiatives but characterized as ``hypothetical''. We have explored the feasibility of obtaining clues to functions of such proteins by means of comparative analysis with cupins of known structure and function. Methodology/Principal Findings: A 3-D structure-based phylogenetic approach was undertaken. Interestingly, a dendrogram generated solely on the basis of structural dissimilarity measure at the level of domain folds was found to cluster functionally similar members. This clustering also reflects an independent evolution of the two domains in bicupins. Close examination of structural superposition of members across various functional clusters reveals structural variations in regions that not only form the active site pocket but are also involved in interaction with another domain in the same polypeptide or in the oligomer. Conclusions/Significance: Structure-based phylogeny of cupins can influence identification of functions of proteins of yet unknown function with cupin fold. This approach can be extended to other proteins with a common fold that show high evolutionary divergence. This approach is expected to have an influence on the function annotation in structural genomics initiatives.

Mechanical response of the tympanal membranes of the tree cricket Oecanthus henryi

Crickets have two tympanal membranes on the tibiae of each foreleg. Among several field cricket species of the genus Gryllus (Gryllinae), the posterior tympanal membrane (PTM) is significantly larger than the anterior membrane (ATM). Laser Doppler vibrometric measurements have shown that the smaller ATM does not respond as much as the PTM to sound. Hence the PTM has been suggested to be the principal tympanal acoustic input to the auditory organ. In tree crickets (Oecanthinae), the ATM is slightly larger than the PTM. Both membranes are structurally complex, presenting a series of transverse folds on their surface, which are more pronounced on the ATM than on the PTM. The mechanical response of both membranes to acoustic stimulation was investigated using microscanning laser Doppler vibrometry. Only a small portion of the membrane surface deflects in response to sound. Both membranes exhibit similar frequency responses, and move out of phase with each other, producing compressions and rarefactions of the tracheal volume backing the tympanum. Therefore, unlike field crickets, tree crickets may have four instead of two functional tympanal membranes. This is interesting in the context of the outstanding question of the role of spiracular inputs in the auditory system of tree crickets.

Characterization of LRRTM and NGR gene families: Expression and functions

Some leucine-rich repeat (LRR) -containing membrane proteins are known regulators of neuronal growth and synapse formation. In this work I characterize two gene families encoding neuronal LRR membrane proteins, namely the LRRTM (leucine-rich repeat, transmembrane neuronal) and NGR (Nogo-66 receptor) families. I studied LRRTM and NGR family member's mRNA tissue distribution by RT-PCR and by in situ hybridization. Subcellular localization of LRRTM1 protein was studied in neurons and in non-neuronal cells. I discovered that LRRTM and NGR family mRNAs are predominantly expressed in the nervous system, and that each gene possesses a specific expression pattern. I also established that LRRTM and NGR family mRNAs are expressed by neurons, and not by glial cells. Within neurons, LRRTM1 protein is not transported to the plasma membrane; rather it localizes to endoplasmic reticulum. Nogo-A (RTN4), MAG, and OMgp are myelin-associated proteins that bind to NgR1 to limit axonal regeneration after central nervous system injury. To better understand the functions of NgR2 and NgR3, and to explore the possible redundancy in the signaling of myelin inhibitors of neurite growth, I mapped the interactions between NgR family and the known and candidate NgR1 ligands. I identified high-affinity interactions between RTN2-66, RTN3-66 and NgR1. I also demonstrate that Rtn3 mRNA is expressed in the same glial cell population of mouse spinal cord white matter as Nogo-A mRNA, and thus it could have a role in myelin inhibition of axonal growth. To understand how NgR1 interacts with multiple structurally divergent ligands, I aimed first to map in more detail the nature of Nogo-A:NgR1 interactions, and then to systematically map the binding sites of multiple myelin ligands in NgR1 by using a library of NgR1 expression constructs encoding proteins with one or multiple surface residues mutated to alanine. My analysis of the Nogo-A:NgR1 -interactions revealed a novel interaction site between the proteins, suggesting a trivalent Nogo-A:NgR1-interaction. Our analysis also defined a central binding region on the concave side of NgR1's LRR domain that is required for the binding of all known ligands, and a surrounding region critical for binding MAG and OMgp. To better understand the biological role of LRRTMs, I generated Lrrtm1 and Lrrtm3 knock out mice. I show here that reporter genes expressed from the targeted loci can be used for maping the neuronal connections of Lrrtm1 and Lrrtm3 expressing neurons in finer detail. With regard to LRRTM1's role in humans, we found a strong association between a 70 kb-spanning haplotype in the proposed promoter region of LRRTM1 gene and two possibly related phenotypes: left-handedness and schizophrenia. Interestingly, the responsible haplotype was linked to phenotypic variability only when paternally inherited. In summary, I identified two families of neuronal receptor-like proteins, and mapped their expression and certain protein-protein interactions. The identification of a central binding region in NgR1 shared by multiple ligands may facilitate the design and development of small molecule therapeutics blocking binding of all NgR1 ligands. Additionally, the genetic association data suggests that allelic variation upstream of LRRTM1 may play a role in the development of left-right brain asymmetry in humans. Lrrtm1 and Lrrtm3 knock out mice developed as a part of this study will likely be useful for schizophrenia and Alzheimer s disease research.

P-T evolution of Glenelg eclogites, NW Scotland: Did they experience ultrahigh-pressure metamorphism?

Eclogites and their retrogressed equivalents from the eastern unit of the Glenelg-Attadale Inlier in NW Scotland preserve much microstructural evidence that indicates that very high-pressure/temperature eclogite facies conditions were reached, and followed by decompression and hydration during exhumation. Rutile exsolution in garnet and quartz exsolution in omphacite and titanite formed through mineral reactions during high P-T peak metamorphism. Isochemical phase diagrams modeled for samples from three different locations indicate that the outer part of the eastern unit preserves a peak metamorphic condition of c. 850-1000 degrees C at 18-25 kbar, whereas the central part has a similar pressure (c. 23 kbar), but a lower temperature (c. 670 degrees C). Due to the limitations in the phase diagram calculations the estimated P-T conditions represent the minimum conditions attained by the peak metamorphic assemblage, and the pre-exsoived peak assemblage probably stabilized at a higher pressure. This observation is strongly supported by the presence of exsolution microstructures. The present results demonstrate that the eastern unit experienced very high P-T conditions during peak metamorphism and a tight clockwise P-T trajectory and provide the first indication of possible ultrahigh-pressure metamorphism in the Glenelg eclogites. (C) 2009 Elsevier B.V. All rights reserved.

Identification and thermodynamic characterization of molten globule states of periplasmic binding proteins

Molten globule-like intermediates have been shown to occur during protein folding and are thought to be involved in protein translocation and membrane insertion. However, the determinants of molten globule stability and the extent of specific packing in molten globules is currently unclear. Using far- and near-UV CD and intrinsic and ANS fluorescence, we show that four periplasmic binding proteins (LBP, LIVBP, MBP, and RBP) form molten globules at acidic pH values ranging from 3.0 to 3.4. Only two of these (LBP and LIVBP) have similar sequences, but all four proteins adopt similar three-dimensional structures. We found that each of the four molten globules binds to its corresponding ligand without conversion to the native state. Ligand binding affinity measured by isothermal titration calorimetry for the molten globule state of LIVBP was found to be comparable to that of the corresponding native state, whereas for LBP, MBP, and RBP, the molten globules bound ligand with approximately 5-30-fold lower affinity than the corresponding native states. All four molten globule states exhibited cooperative thermal unfolding assayed by DSC. Estimated values of Delta C-p of unfolding show that these molten globule states contain 28-67% of buried surface area relative to the native states. The data suggest that molten globules of these periplasmic binding proteins retain a considerable degree of long range order. The ability of these sequentially unrelated proteins to form highly ordered molten globules may be related to their large size as well as an intrinsic property of periplasmic binding protein folds.

Enhanced adsorption capacity of activated alumina by impregnation with alum for removal of As(V) from water

Alum-impregnated activated alumina (AIAA) was investigated in the present work as an adsorbent for the removal of As(V) from water by batch mode. Adsorption study at different pH values shows that the efficiency of AIAA is much higher than as such activated alumina and is suitable for treatment of drinking water. The adsorption isotherm experiments indicated that the uptake of As(V) increased with increasing As(V) concentration from 1 to 25 mg/l and followed Langmuir-type adsorption isotherm. Speciation diagram shows that in the pH range of 2.8–11.5, arsenate predominantly exists as H2AsO4− and HAsO42− species and hence it is presumed that these are the major species being adsorbed on the surface of AIAA. Intraparticle diffusion and kinetic studies revealed that adsorption of As(V) was due to physical adsorption as well as through intraparticle diffusion. Effect of interfering ions revealed that As(V) sorption is strongly influenced by the presence of phosphate ion. The presence of arsenic on AIAA is depicted from zeta potential measurement, scanning electron microscopy (SEM) and energy-dispersive analysis of X-ray (EDAX) mapping study. Alum-impregnated activated alumina successfully removed As(V) to below 40 ppb (within the permissible limit set by WHO) from water, when the initial concentration of As(V) is 10 mg/l.

Digital Photography in the Diagnosis and Follow-up of Ocular Diseases

Purpose: The aim of the present study was to develop and test new digital imaging equipment and methods for diagnosis and follow-up of ocular diseases. Methods: The whole material comprised 398 subjects (469 examined eyes), including 241 patients with melanocytic choroidal tumours, 56 patients with melanocytic iris tumours, 42 patients with diabetes, a 52-year old patient with chronic phase of VKH disease, a 30-year old patient with an old blunt eye injury, and 57 normal healthy subjects. Digital 50° (Topcon TRC 50 IA) and 45° (Canon CR6-45NM) fundus cameras, a new handheld digital colour videocamera for eye examinations (MediTell), a new subtraction method using the Topcon Image Net Program (Topcon corporation, Tokyo, Japan), a new method for digital IRT imaging of the iris we developed, and Zeiss photoslitlamp with a digital camera body were used for digital imaging. Results: Digital 50° red-free imaging had a sensitivity of 97.7% and two-field 45° and 50° colour imaging a sensitivity of 88.9-94%. The specificity of the digital 45°-50° imaging modalities was 98.9-100% versus the reference standard and ungradeable images that were 1.2-1.6%. By using the handheld digital colour video camera only, the optic disc and central fundus located inside 20° from the fovea could be recorded with a sensitivity of 6.9% for detection of at least mild NPDR when compared with the reference standard. Comparative use of digital colour, red-free, and red light imaging showed 85.7% sensitivity, 99% specificity, and 98.2 % exact agreement versus the reference standard in differentiation of small choroidal melanoma from pseudomelanoma. The new subtraction method showed growth in four of 94 melanocytic tumours (4.3%) during a mean ±SD follow-up of 23 ± 11 months. The new digital IRT imaging of the iris showed the sphincter muscle and radial contraction folds of Schwalbe in the pupillary zone and radial structural folds of Schwalbe and circular contraction furrows in the ciliary zone of the iris. The 52-year-old patient with a chronic phase of VKH disease showed extensive atrophy and occasional pigment clumps in the iris stroma, detachment of the ciliary body with severe ocular hypotony, and shallow retinal detachment of the posterior pole in both eyes. Infrared transillumination imaging and fluorescein angiographic findings of the iris showed that IR translucence (p=0.53), complete masking of fluorescence (p=0.69), presence of disorganized vessels (p=0.32), and fluorescein leakage (p=1.0) at the site of the lesion did not differentiate an iris nevus from a melanoma. Conclusions: Digital 50° red-free and two-field 50° or 45° colour imaging were suitable for DR screening, whereas the handheld digital video camera did not fulfill the needs of DR screening. Comparative use of digital colour, red-free and red light imaging was a suitable method in the differentiation of small choroidal melanoma from different pseudomelanomas. The subtraction method may reveal early growth of the melanocytic choroidal tumours. Digital IRT imaging may be used to study changes of the stroma and posterior surface of the iris in various diseases of the uvea. It contributed to the revealment of iris atrophy and serous detachment of the ciliary body with ocular hypotony together with the shallow retinal detachment of the posterior pole as new findings of the chronic phase of VKH disease. Infrared translucence and angiographic findings are useful in differential diagnosis of melanocytic iris tumours, but they cannot be used to determine if the lesion is benign or malignant.

Quality assessment of CdZnTe (Zn similar to 4 %) crystals

We have studied the as grown and annealed CdZnTe (Zn similar to 4 %) crystals for the assessment of their crystalline quality. As grown crystals suffer from tellurium precipitates and cadmium vacancies, which are inherent, due to retrograde solid solubility curve in the phase diagram. This is reflected in the Fourier transform infrared (FTIR) spectra over the 400 - 4500 cm(-1) range by a strong absorption around 2661 cm(-1) which corresponds to the band gap of tellurium confirming their presence, where-as a monotonic decrease in the transmission with the decrease in wave number indicates the presence of cadmium vacancies. Obviously the presence of Cd vacancies lead to the formation of tellurium precipitates confirming their presence. Annealed samples under cadmium + zinc ambient at 650 degrees C for 6 hours show an improvement in the transmission over the same range. This can be attributed to thermo-migration of tellurium precipitates and hence bonding with Cd or Zn to form CdZnTe. This is further supported by the reduced full width at half maximum in the X-ray diffraction rocking curve of these CdZnTe crystals. Cadmium annealing although can passivate Cd vacancy related defects and reduce the Te precipitates, as is observed in our low temperature Photoluminescence (PL) spectra, alone may not be sufficient possibly due to the loss of Zn. Vacuum annealing at 650 degrees C for 6 hours further deteriorated the material quality as is reflected in the low temperature PL spectra by the introduction of a new defect band around 0.85 eV and reduced IR transmission.

Phase Diagram for the System RuO2-TiO2 in Air

There are conflicting reports in the literature regarding solid solubility in the system RuO2-TiO2. To resolve this issue a few experiments were conducted in air at 1673, 1723, and 1773 K. The results show limited terminal solid solubility. There is an extended solid-state miscibility gap that intersects the decomposition curve for the RuO2-rich solid solution generating a peritectoid reaction at 1698 K. The measured equilibrium compositions of the solid solutions are used to develop a thermodynamic description of the oxide solid solution with rutile structure. Using the subregular solution model, the enthalpy of mixing can be represented by the expression, Delta H-M/J center dot mol(-1) = XTiO2XRuO2 ( 34,100X(TiO2) + 30,750X(RuO2)). The binodal and spinodal curves and T-X phase diagram in air are computed using this datum and Gibbs energy of formation of RuO2 available in the literature. The computed results suggest that equilibrium was not attained during solubility measurements at lower temperatures reported in the literature.

Phase-Field Simulation of Fusion Interface Events during Solidification of Dissimilar Welds: Effect of Composition Inhomogeneity

We investigate the events near the fusion interfaces of dissimilar welds using a phase-field model developed for single-phase solidification of binary alloys. The parameters used here correspond to the dissimilar welding of a Ni/Cu couple. The events at the Ni and the Cu interface are very different, which illustrate the importance of the phase diagram through the slope of the liquidus curves. In the Ni side, where the liquidus temperature decreases with increasing alloying, solutal melting of the base metal takes place; the resolidification, with continuously increasing solid composition, is very sluggish until the interface encounters a homogeneous melt composition. The growth difficulty of the base metal increases with increasing initial melt composition, which is equivalent to a steeper slope of the liquidus curve. In the Cu side, the initial conditions result in a deeply undercooled melt and contributions from both constrained and unconstrained modes of growth are observed. The simulations bring out the possibility of nucleation of a concentrated solid phase from the melt, and a secondary melting of the substrate due to the associated recalescence event. The results for the Ni and Cu interfaces can be used to understand more complex dissimilar weld interfaces involving multiphase solidification.