The Global Engineer : Incorporating global skills within UK higher education of engineers

Background. The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. To understand the evolution of MARV at the codon level, we report a comprehensive analysis of synonymous codon usage patterns in MARV genomes. Multiple codon analysis approaches and statistical methods were performed to determine overall codon usage patterns, biases in codon usage, and influence of various factors, including mutation pressure, natural selection, and its two hosts, Homo sapiens and Rousettus aegyptiacus. Results. Nucleotide composition and relative synonymous codon usage (RSCU) analysis revealed that MARV shows mutation bias and prefers U- and A-ended codons to code amino acids. Effective number of codons analysis indicated that overall codon usage among MARV genomes is slightly biased. The Parity Rule 2 plot analysis showed that GC and AU nucleotides were not used proportionally which accounts for the presence of natural selection. Codon usage patterns of MARV were also found to be influenced by its hosts. This indicates that MARV have evolved codon usage patterns that are specific to both of its hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU patterns was found to be dominant compared with that from H. sapiens. Overall, mutation pressure was found to be the most important and dominant force that shapes codon usage patterns in MARV. Conclusions. To our knowledge, this is the first detailed codon usage analysis of MARV and extends our understanding of the mechanisms that contribute to codon usage and evolution of MARV

Genetics And Interrelationship of Yield and Yield Related Attributes in Some Genotypes of Safflower (Carthamus Tinctorius L.) Under Rainfed Conditions

In order to estimate variability, heritability, genetic advance and relationship of grain yield with other yield related attributes, the experiments were carried out in field research Area of Barani Agricultural Research Institute, Chakwal, Pakistan during two rabi growing seasons 2011-12 and 2012-13. The experimental materials were comprised of 40 genotypes of safflower and were sown in randomized complete block design with three replications each year. The analysis of variance showed that all the safflower genotypes were significantly different for all the traits studied except days to physiological maturity. Among the attributes studied the estimates of phenotypic coefficient of variation (PCV) were generally higher than the genetic coefficient of variation (GCV).  Highest GCV was found in grain filing rate plant-1 (49.34 & 48.25) followed by seed yield plant-1 (49.09 & 48.18) during 2011-12 & 2012-13 respectively. Grain filing rate plant-1 showed maximum PCV (49.78 & 48.96) followed by seed yield plant-1 (49.64 & 49.44) during both years (2011-12 & 2012-13) respectively. The high heritability coupled with high genetic advance was measured in biological yield plant-1, harvest index (%), number of heads plant-1, and seed yield plant-1. These results revealed that high estimates of heritability and genetic advance for these traits would be helpful for the plant breeders to select the suitable combination and to achieve the enviable level of seed yield potential in safflower under arid environment conditions. The correlation results of two year studies revealed that seed yield plant-1 had significant and positive relationship with days to maturity, plant height, biological yield plant-1, number of seeds head-1, 1000-grain weight, grain filing rate plant-1, effective head weight, number of primary branches  plant-1 and plant height. On the other hand, days to 50% flowering, days to physiological maturity, number of seeds head-1, seed weight head-1 and 1000- grain weight showed low heritability with low genetic advance. Key words: Safflower, Rainfed, Variability, Heritability, Genetic Advance, Correlatio

Performance Based Evaluation and Selection of Different Promising Lines of Rapeseed (Brassica Napus L.) for the Shattering Tolerance

To evaluate the ten promising lines of Brassica napus against the shattering tolerance, the experiments were carried out in split plot design in the research area of Barani Agricultural Research Institute; Chakwal, Pakistan during two rabi growing season 2011-12 & 2012-13 under rainfed conditions. The main plot was harvested in five different harvesting dates including: HarD1 = Harvesting at physiological maturity of crop, HarD2= 7 days after the first harvesting of each promising line, HarD3= 15 days after the first harvesting of each promising line, HarD4= 21 days after the first harvesting of each promising line, HarD5= 30 days after the first harvesting of each promising line. The difference of grain yield (kg/ha) of each promising line in different harvesting dates with compare to its grain yield (kg/ha) in first harvesting date (HarD1-HarDi) were measured as indices of shattering. The combine analysis of variance of two year revealed that all the promising lines were significant different for harvesting date, harvesting date x promising lines interaction effect and also year and its interaction effects to each study factors. In the present experiment, the promising line 12CBN008 & 10CBN004 had grain yield 1089 kg/ha & 897 kg/ha respectively. The significant difference of genotypes x harvesting dates confirmed different level of shattering of all promising lines in different harvesting dates. The magnitude of grain yield shattering loss was increased in 4th and 5th harvesting dates. On the basis of shattering tolerance among all the promising lines the 11CBN010 was more tolerant to shattering and 11CBN005 were relatively more susceptible to shattering. Keywords: Rapeseed, Harvesting date, Shattering toleranc

Helium beam shadowing for high spatial resolution patterning of antibodies on microstructured diagnostic surfaces

We have developed a technique for the high-resolution, self-aligning, and high-throughput patterning of antibody binding functionality on surfaces by selectively changing the reactivity of protein-coated surfaces in specific regions of a workpiece with a beam of energetic helium particles. The exposed areas are passivated with bovine serum albumin (BSA) and no longer bind the antigen. We demonstrate that patterns can be formed (1) by using a stencil mask with etched openings that forms a patterned exposure, or (2) by using angled exposure to cast shadows of existing raised microstructures on the surface to form self-aligned patterns. We demonstrate the efficacy of this process through the patterning of anti-lysozyme, anti-Norwalk virus, and anti-Escherichia coli antibodies and the subsequent detection of each of their targets by the enzyme-mediated formation of colored or silver deposits, and also by binding of gold nanoparticles. The process allows for the patterning of three-dimensional structures by inclining the sample relative to the beam so that the shadowed regions remain unaltered. We demonstrate that the resolution of the patterning process is of the order of hundreds of nanometers, and that the approach is well-suited for high throughput patterning

High-Throughput Top-Down Fabrication of Uniform Magnetic Particles

Ion Beam Aperture Array Lithography was applied to top-down fabrication of large dense (108–109 particles/cm2) arrays of uniform micron-scale particles at rates hundreds of times faster than electron beam lithography. In this process, a large array of helium ion beamlets is formed when a stencil mask containing an array of circular openings is illuminated by a broad beam of energetic (5–8 keV) ions, and is used to write arrays of specific repetitive patterns. A commercial 5-micrometer metal mesh was used as a stencil mask; the mesh size was adjusted by shrinking the stencil openings using conformal sputter-deposition of copper. Thermal evaporation from multiple sources was utilized to form magnetic particles of varied size and thickness, including alternating layers of gold and permalloy. Evaporation of permalloy layers in the presence of a magnetic field allowed creation of particles with uniform magnetic properties and pre-determined magnetization direction. The magnetic properties of the resulting particles were characterized by Vibrating Sample Magnetometry. Since the orientation of the particles on the substrate before release into suspension is known, the orientation-dependent magnetic properties of the particles could be determined

Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses

<div><p>Chikungunya virus (CHIKV) is an arthropod-borne virus of the family <i>Togaviridae</i> that is transmitted to humans by <i>Aedes</i> spp. mosquitoes. Its genome comprises a 12 kb single-strand positive-sense RNA. In the present study, we report the patterns of synonymous codon usage in 141 CHIKV genomes by calculating several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C and A-ended. A comparative analysis of RSCU between CHIKV and its hosts showed that codon usage patterns of CHIKV are a mixture of coincidence and antagonism. Similarity index analysis showed that the overall codon usage patterns of CHIKV have been strongly influenced by <i>Pan troglodytes</i> and <i>Aedes albopictus</i> during evolution. The overall codon usage bias was low in CHIKV genomes, as inferred from the analysis of effective number of codons (ENC) and codon adaptation index (CAI). Our data suggested that although mutation pressure dominates codon usage in CHIKV, patterns of codon usage in CHIKV are also under the influence of natural selection from its hosts and geography. To the best of our knowledge, this is first report describing codon usage analysis in CHIKV genomes. The findings from this study are expected to increase our understanding of factors involved in viral evolution, and fitness towards hosts and the environment.</p></div

The synonymous codon usage patterns of CHIKV, its hosts and transmission vectors.

<p>AA: amino acid, HS: <i>H. sapiens</i>, AG: <i>A. aegypti</i>, AB: <i>A. albopictus</i>, PT: <i>P. troglodytes</i>. Preferred codons of CHIKV, <i>H. sapiens</i>, <i>A. aegypti</i>, <i>A. albopictus and P. troglodytes</i> are shown in bold.</p>a<p>Amino acids with A/U-ended preferred codons in CHIKV.</p>b<p>Amino acids with G/C-ended preferred codons in CHIKV.</p>c<p>Amino acids with A/U-ended preferred codons in CHIKV.</p>d<p>Amino acids with G/C-ended preferred codons in CHIKV.</p