Type II beta-turn conformation of pivaloyl-L-prolyl-alpha-aminoisobutyryl-N-methylamide: Theoretical, spectroscopic, and X-ray studies

Pivaloyl-L-Pro-Aib-N-methylamide has been shown to possess one intramolecular hydrogen bond in (CD3)2SO solution, by 1H-nmr methods, suggesting the existence of beta -turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II beta-turn conformations are about 2 kcal mol-1 more stable than Type III structures. A crystallographic study has established the Type II beta-turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, beta = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II -turn conformation is stabilized by an intramolecular 4 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are Pro = -57.8°, Pro = 139.3°, Aib = 61.4°, and Aib = 25.1°. The Type II beta-turn conformation for Pro-Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.

Note on the one-parameter scaling theory of localisation

The necessary and sufficient condition for the existence of the one-parameter scale function, the /Munction, is obtained exactly. The analysis reveals certain inconsistency inherent in the scaling theory, and tends to support Motts’ idea of minimum metallic conductivity.

Note on the one-parameter scaling theory of localisation

The necessary and sufficient condition for the existence of the one-parameter scale function, the /Munction, is obtained exactly. The analysis reveals certain inconsistency inherent in the scaling theory, and tends to support Motts’ idea of minimum metallic conductivity.

Foldable compatibility matrix for the folding of programmable logic arrays

This paper describes a switching theoretic algorithm for the folding of programmable logic arrays (PLA). The algorithm is valid for both column and row folding, although it has been presented considering only the simple column folding. The pairwise compatibility relations among all the pairs of the columns of the PLA are mapped into a square matrix, called the compatibility matrix of the PLA. A foldable compatibility matrix (FCM), a new concept introduced by the author, is then derived from the compatibility matrix. A new theorem called the folding theorem is then proved. The theorem states that the existence of an m by 2m FCM is both necessary and sufficient to fold 2m columns of the n column PLA (2m ≤ n). Once an FCM is obtained, the ordered pairs of foldable columns and the re-ordering of the rows are readily determined.

A molecular dynamics investigation of the structure of PbO---PbF2 glasses*1

The structure of PbO---PbF2 glasses has been studied using molecular dynamics (MD). The existence of [OPb4] structural units is observed over the entire glass-forming range, in conformity with a model proposed earlier based on various structural investigations of this system. Various other features of the structural model are also supported by the MD calculations.

Determination of management units for grey mackerel fisheries in northern Australia.

The requirement for Queensland, Northern Territory and Western Australian jurisdictions to ensure sustainable harvest of fish resources and their optimal use relies on robust information on the resource status. For grey mackerel (Scomberomorus semifasciatus) fisheries, each of these jurisdictions has their own management regime in their corresponding waters. The lack of information on stock structure of grey mackerel, however, means that the appropriate spatial scale of management is not known. As well, fishers require assurance of future sustainability to encourage investment and long-term involvement in a fishery that supplies lucrative overseas markets. These management and fisher-unfriendly circumstances must be viewed in the context of recent 3-fold increases in catches of grey mackerel along the Queensland east coast, combined with significant and increasing catches in other parts of the species' northern Australian range. Establishing the stock structure of grey mackerel would also immensely improve the relevance of resource assessments for fishery management of grey mackerel across northern Australia. This highlighted the urgent need for stock structure information for this species. The impetus for this project came from the strategic recommendations of the FRDC review by Ward and Rogers (2003), "Northern mackerel (Scombridae: Scomberomorus): current and future research needs" (Project No. 2002/096), which promoted the urgency for information on the stock structure of grey mackerel. In following these recommendations this project adopted a multi-technique and phased sampling approach as carried out by Buckworth et al (2007), who examined the stock structure of Spanish mackerel, Scomberomorus commerson, across northern Australia. The project objectives were to determine the stock structure of grey mackerel across their northern Australian range, and use this information to define management units and their appropriate spatial scales. We used multiple techniques concurrently to determine the stock structure of grey mackerel. These techniques were: genetic analyses (mitochondrial DNA and microsatellite DNA), otolith (ear bones) isotope ratios, parasite abundances, and growth parameters. The advantage of using this type of multi-technique approach was that each of the different methods is informative about the fish’s life history at different spatial and temporal scales. Genetics can inform about the evolutionary patterns as well as rates of mixing of fish from adjacent areas, while parasites and otolith microchemistry are directly influenced by the environment and so will inform about the patterns of movement during the fishes lifetime. Growth patterns are influenced by both genetic and environmental factors. Due to these differences the use of these techniques concurrently increases the likelihood of detecting different stocks where they exist. We adopted a phased sampling approach whereby sampling was carried out at broad spatial scales in the first year: east coast, eastern Gulf of Carpentaria (GoC), western GoC, and the NW Northern Territory (NW NT). By comparing the fish samples from each of these locations, and using each of the techniques, we tested the null hypothesis that grey mackerel were comprised of a single homogeneous population across northern Australia. Having rejected the null hypothesis we re-sampled the 1st year locations to test for temporal stability in stock structure, and to assess stock structure at finer spatial scales. This included increased spatial coverage on the east coast, the GoC, and WA. From genetic approaches we determined that there at least four genetic stocks of grey mackerel across northern Australia: WA, NW NT (Timor/Arafura), the GoC and the east Grey mackerel management units in northern Australia ix coast. All markers revealed concordant patterns showing WA and NW NT to be clearly divergent stocks. The mtDNA D-loop fragment appeared to have more power to resolve stock boundaries because it was able to show that the GoC and east coast QLD stocks were genetically differentiated. Patterns of stock structure on a finer scale, or where stock boundaries are located, were less clear. From otolith stable isotope analyses four major groups of S. semifasciatus were identified: WA, NT/GoC, northern east coast and central east coast. Differences in the isotopic composition of whole otoliths indicate that these groups must have spent their life history in different locations. The magnitude of the difference between the groups suggests a prolonged separation period at least equal to the fish’s life span. The parasite abundance analyses, although did not include samples from WA, suggest the existence of at least four stocks of grey mackerel in northern Australia: NW NT, the GoC, northern east coast and central east coast. Grey mackerel parasite fauna on the east coast suggests a separation somewhere between Townsville and Mackay. The NW NT region also appears to comprise a separate stock while within the GoC there exists a high degree of variability in parasite faunas among the regions sampled. This may be due to 1. natural variation within the GoC and there is one grey mackerel stock, or 2. the existence of multiple localised adult sub-stocks (metapopulations) within the GoC. Growth parameter comparisons were only possible from four major locations and identified the NW NT, the GoC, and the east coast as having different population growth characteristics. Through the use of multiple techniques, and by integrating the results from each, we were able to determine that there exist at least five stocks of grey mackerel across northern Australia, with some likelihood of additional stock structuring within the GoC. The major management units determined from this study therefore were Western Australia, NW Northern Territory (Timor/Arafura), the Gulf of Carpentaria, northern east Queensland coast and central east Queensland coast. The management implications of these results indicate the possible need for management of grey mackerel fisheries in Australia to be carried out on regional scales finer than are currently in place. In some regions the spatial scales of management might continue as is currently (e.g. WA), while in other regions, such as the GoC and the east coast, managers should at least monitor fisheries on a more local scale dictated by fishing effort and assess accordingly. Stock assessments should also consider the stock divisions identified, particularly on the east coast and for the GoC, and use life history parameters particular to each stock. We also emphasise that where we have not identified different stocks does not preclude the possibility of the occurrence of further stock division. Further, this study did not, nor did it set out to, assess the status of each of the stocks identified. This we identify as a high priority action for research and development of grey mackerel fisheries, as well as a management strategy evaluation that incorporates the conclusions of this work. Until such time that these priorities are addressed, management of grey mackerel fisheries should be cognisant of these uncertainties, particularly for the GoC and the Queensland east coast.

Estimating and influencing the duration of weed eradication programmes

1. Weed eradication efforts often must be sustained for long periods owing to the existence of persistent seed banks, among other factors. Decision makers need to consider both the amount of investment required and the period over which investment must be maintained when determining whether to commit to (or continue) an eradication programme. However, a basis for estimating eradication programme duration based on simple data has been lacking. Here, we present a stochastic dynamic model that can provide such estimates. 2. The model is based upon the rates of progression of infestations from the active to the monitoring state (i.e. no plants detected for at least 12 months), rates of reversion of infestations from monitoring to the active state and the frequency distribution of time since last detection for all infestations. Isoquants that illustrate the combinations of progression and reversion parameters corresponding to eradication within different time frames are generated. 3. The model is applied to ongoing eradication programmes targeting branched broomrape Orobanche ramosa and chromolaena Chromolaena odorata. The minimum periods in which eradication could potentially be achieved were 22 and 23 years, respectively. On the basis of programme performance until 2008, however, eradication is predicted to take considerably longer for both species (on average, 62 and 248 years, respectively). Performance of the branched broomrape programme could be best improved through reducing rates of reversion to the active state; for chromolaena, boosting rates of progression to the monitoring state is more important. 4. Synthesis and applications. Our model for estimating weed eradication programme duration, which captures critical transitions between a limited number of states, is readily applicable to any weed.Aparticular strength of the method lies in its minimal data requirements. These comprise estimates of maximum seed persistence and infested area, plus consistent annual records of the detection (or otherwise) of the weed in each infestation. This work provides a framework for identifying where improvements in management are needed and a basis for testing the effectiveness of alternative tactics. If adopted, our approach should help improve decision making with regard to eradication as a management strategy.

Periodic Rayleigh waves of finite amplitude on an isotropic solid

Existence of a periodic progressive wave solution to the nonlinear boundary value problem for Rayleigh surface waves of finite amplitude is demonstrated using an extension of the method of strained coordinates. The solution, obtained as a second-order perturbation of the linearized monochromatic Rayleigh wave solution, contains harmonics of all orders of the fundamental frequency. It is shown that the higher harmonic content of the wave increases with amplitude, but the slope of the waveform remains finite so long as the amplitude is less than a critical value.

An electron microscopic study of quasicrystals in a quaternary alloy : Mg32(Al, Zn, Cu)49

The discovery of a solid exhibiting m 3 5 point group symmetry by Shechtman et. al. (l) in a rapidly solidified Al-14at%Mn alloy has activated intensive studies of a new class of solids, termed as quasicrystals (2). While the original discovery reported the existence of quasicrystals in AI-Mn. AI-Fe and AI-Cr alloys, subsequent work has revealed their existence in Mg-Zn-Al(3,4), Mg-A]-Cu(5), AI-Mn-Si(6) and Ti-Ni-V(7) alloys (Table l).

Investigations Of Glasses In The System Pbo-Pbf2

Glass formation in the system PbO–PbF2 has been investigated. The structure of these glasses has been studied using X-ray diffraction. Densities, heat capacities, glass-transition and crystallization temperatures and Vicker's microhardnesses have been measured. D.c. conductivities of these glasses have also been measured as a function of temperature. A structural model has been developed which suggests the existence of [PbO2F4]-type units over the entire composition range. It is suggested that covalent linkages of the type—O—Pb—O— play a crucial role in determining the composition limits to glass formation. The structural model has been shown to be consistent with other physical properties of the glasses.

Sensing Shape Recovery Using Conductivity Noise in Thin Films of NiTi Shape Memory Alloys

Low frequency fluctuations in the electrical resistivity, or noise, have been used as a sensitive tool to probe into the temperature driven martensite transition in dc magnetron sputtered thin films of nickel titanium shape-memory alloys. Even in the equilibrium or static case, the noise magnitude was more than nine orders of magnitude larger than conventional metallic thin films and had a characteristic dependence on temperature. We observe that the noise while the temperature is being ramped is far larger as compared to the equilibrium noise indicating the sensitivity of electrical resistivity to the nucleation and propagation of domains during the shape recovery. Further, the higher order statistics suggests the existence of long range correlations during the transition. This new characterization is based on the kinetics of disorder in the system and separate from existing techniques and can be integrated to many device applications of shape memory alloys for in-situ shape recovery sensing.

Methicillin Resistance In Staphylococci : Horizontal Transfer of Mobile Genetic Element (SCCmec) Between Staphylococcal Species

Regardless of the existence of antibiotics, infectious diseases are the leading causes of death in the world. Staphylococci cause many infections of varying severity, although they can also exist peacefully in many parts of the human body. Most often Staphylococcus aureus colonises the nose, and that colonisation is considered to be a risk factor for spread of this bacterium. S. aureus is considered to be the most important Staphylococcus species. It poses a challenge to the field of medicine, and one of the most problematic aspects is the drastic increase of the methicillin-resistant S. aureus (MRSA) strains in hospitals and community world-wide, including Finland. In addition, most of the clinical coagulase-negative staphylococcus (CNS) isolates express resistance to methicillin. Methicillin-resistance in S. aureus is caused by the mecA gene that encodes an extra penicillin-binding protein (PBP) 2a. The mecA gene is found in a mobile genomic island called staphylococcal chromosome cassette mec (SCCmec). The SCCmec consists of the mec gene and cassette chromosome recombinase (ccr)gene complexes. The areas of the SCCmec element outside the ccr and mec complex are known as the junkyard J regions. So far, eight types of SCCmec(SCCmec I- SCCmec VIII) and a number of variants have been described. The SCCmec island is an acquired element in S. aureus. Lately, it appears that CNS might be the storage place of the SCCmec that aid the S. aureus by providing it with the resistant elements. The SCCmec is known to exist only in the staphylococci. The aim of the present study was to investigate the horizontal transfer of SCCmec between the S. aureus and CNS. One specific aim was to study whether or not some methicillin-sensitive S. aureus (MSSA) strains are more inclined to receive the SCCmec than others. This was done by comparing the genetic background of clinical MSSA isolates in the health care facilities of the Helsinki and Uusimaa Hospital District in 2001 to the representatives of the epidemic MRSA (EMRSA) genotypes, which have been encountered in Finland during 1992-2004. Majority of the clinical MSSA strains were related to the EMRSA strains. This finding suggests that horizontal transfer of SCCmec from unknown donor(s) to several MSSA background genotypes has occurred in Finland. The molecular characteristics of representative clinical methicillin-resistant S. epidermidis (MRSE) isolates recovered in Finnish hospitals between 1990 and 1998 were also studied, examining their genetic relation to each other and to the internationally recognised MRSE clones as well, so as to ascertain the common traits between the SCCmec elements in MRSE and MRSA. The clinical MRSE strains were genetically related to each other; eleven PFGE types were associated with sequence type ST2 that has been identified world-wide. A single MRSE strain may possess two SCCmec types III and IV, which were recognised among the MRSA strains. Moreover, six months after the onset of an outbreak of MRSA possessing a SCCmec type V in a long-term care facility in Northern Finland (LTCF) in 2003, the SCCmec element of nasally carried methicillin-resistant staphylococci was studied. Among the residents of a LTCF, nasal carriage of MR-CNS was common with extreme diversity of SCCmec types. MRSE was the most prevalent CNS species. Horizontal transfer of SCCmec elements is speculated to be based on the sharing of SCCmec type V between MRSA and MRSE in the same person. Additionally, the SCCmec element of the clinical human S. sciuri isolates was studied. Some of the SCCmec regions were present in S. sciuri and the pls gene was common in it. This finding supports the hypothesis of genetic exchange happening between staphylococcal species. Evaluation of the epidemiology of methicillin-resistant staphylococcal colonisation is necessary in order to understand the apparent emergence of these strains and to develop appropriate control strategies. SCCmec typing is essential for understanding the emergence of MRSA strains from CNS, considering that the MR-CNS may represent the gene pool for the continuous creation of new SCCmec types from which MRSA might originate.

Molecular Genetic Background of Tumours in Hereditary Leiomyomatosis and Renal Cell Cancer Syndrome

Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC) is a hereditary tumour predisposition syndrome. Its phenotype includes benign cutaneous and uterine leiomyomas (CLM, ULM) with high penetrance and rarer renal cell cancer (RCC), most commonly of papillary type 2 subtype. Over 130 HLRCC families have been identified world-wide but the RCC phenotype seems to concentrate in families from Finland and North America for unknown reasons. HLRCC is caused by heterozygous germline mutations in the fumarate hydratase (FH) gene. FH encodes the enzyme fumarase from mitochondrial citric acid cycle. Fumarase enzyme activity or type or site of the FH mutation are unassociated with disease phenotype. The strongest evidence for tumourigenesis mechanism in HLRCC supports a hypoxia inducible factor driven process called pseudohypoxia resulting from accumulation of the fumarase substrate fumarate. In this study, to assess the importance of gene- or exon-level deletions or amplifications of FH in patients with HLRCC-associated phenotypes, multiplex ligation-dependent probe amplification (MLPA) method was used. One novel FH mutation, deletion of exon 1, was found in a Swedish male patient with an evident HLRCC phenotype with CLM, RCC, and a family history of ULM and RCC. Six other patients with CLM and 12 patients with only RCC or uterine leiomyosarcoma (ULMS) remained FH mutation-negative. These results suggest that copy number aberrations of FH or its exons are an infrequent cause of HLRCC and that only co-occurrence of benign tumour types justifies FH-mutation screening in RCC or ULMS patients. Determination of the genomic profile of 11 HLRCC-associated RCCs from Finnish patients was performed by array comparative genomic hybridization. The most common copy number aberrations were gains of 2, 7, and 17 and losses of 13q12.3-q21.1, 14, 18, and X. When compared to aberrations of sporadic papillary RCCs, HLRCC-associated RCCs harboured a distinct DNA copy number profile and lacked many of the changes characterizing the sporadic RCCs. The findings suggest a divergent molecular pathway for tumourigenesis of papillary RCCs in HLRCC. In order to find a genetic modifier of RCC risk in HLRCC, genome-wide linkage and identical by descent (IBD) analysis studies were performed in Finnish HLRCC families with microsatellite marker mapping and SNP-array platforms. The linkage analysis identified only one locus of interest, the FH gene locus in 1q43, but no mutations were found in the genes of the region. IBD analysis yielded no convincing haplotypes shared by RCC patients. Although these results do not exclude the existence of a genetic modifier for RCC risk in HLRCC, they emphasize the role of FH mutations in the malignant tumourigenesis of HLRCC. To study the benign tumours in HLRCC, genome-wide DNA copy number and gene expression profiles of sporadic and HLRCC ULMs were defined with modern SNP- and gene-expression array platforms. The gene expression array suggests novel genes involved in FH-deficient ULM tumourigenesis and novel genes with putative roles in propagation of sporadic ULM. Both the gene expression and copy number profiles of HLRCC ULMs differed from those of sporadic ULMs indicating distinct molecular basis of the FH-deficient HLRCC tumours.

Use of transverse polarization to probe R-parity violating supersymmetry at ILC

In supersymmetric theories with R-parity violation, squarks and sleptons can mediate Standard Model fermion–fermion scattering processes. These scalar exchanges in e+e− initiated reactions can give new signals at future linear colliders. We explore use of transverse beam polarization in the study of these signals in the process View the MathML source. We highlight certain asymmetries, which can be constructed due to the existence of the transverse beam polarization, which offer discrimination from the Standard Model (SM) background and provide increased sensitivity to the R-parity violating couplings.

Biology, Management and Genetic Stock Structure of Mangrove Jack, (Lutjanus argentimaculatus) in Australia.

This project has contributed to the ecologically sustainable management of mangrove jack in Australia by providing comprehensive information on its biology, habitat requirements, population parameters and stock structure. Specifically, the project has resulted in an enhanced understanding of the life history of Australian mangrove jack, the levels of exploitation in its local fishery and the likely existence of a single genetic stock throughout Queensland.