Rolling circle amplification assays to detect members of the family Anelloviridae from pig and human biological samples

The present study describes the optimization of Rolling Circle Amplification (RCA) assays to detect members of the family Anelloviridae from pig and human sera. Standard RCA involves the prolonged elongation of random primers bound to a circular DNA template by Phi29 DNA polymerase. The RCA products, that are tandem repeat copies of the viral complete genome, were used for the Sequence Independent Single Primer Amplification (SISPA) method, based on the use of endonuclease restriction of target sequences. These products were separated on agarose gel and different length products were ligated to specific linkers followed by PCR amplification and sequencing. With this combined approach it was possible to detect Torque teno sus virus (TTSuV) 2 in swine. Afterwards, a specific RCA technique was optimized. RCA was first carried out using short Anellovirus specific primers based on a highly conserved region among available anellovirus full-length genomes. Then, products from RCA were used as templates to amplify full-length genomes with Anellovirus specific PCR. Amplification products were run on agarose gel and full-length genomes were isolated based on the expected size. With this novel Anello-RCA/PCR approach it was possible to detect TTSuV 1 and 2 in swine and Torque teno virus (TTV) in human serum samples, which tested previously negative by conventional PCR. Based on these results, we demonstrated that combined RCA-SISPA previously set up for other species is applicable also for TTV DNA detection in swine, and Anello-RCA/PCR is a useful technique to discover members of the genus Iotatorquevirus and Alphatorquevirus. In comparison with the standard RCA combined with the SISPA approach, the Anello-RCA/PCR assay is faster and cheaper, resulting in full-length genomic sequences of Anelloviruses. Furthermore, the technique could be applicable to other species whose TTVs have not been fully characterized as yet, increasing the probability to obtain new viral species belonging to the family Anelloviridae

The characterization of recycled concrete aggregate as filter in removal of phosphorus

Phosphorus (P) is one of the key nutrients that lead to eutrophication problem in surface water. However, the existing conventional wastewater treatment system to remove phosphorus is expensive and require a complex process. Therefore, a system using low cost and environmental friendly should be practiced to overcome this problem. Recycled concrete aggregate (RCA) used as a filter system emerged as an alternative technology for phosphorus removal. This can overcome the problem of construction site waste by converting the waste into something valuable products. Thus, this study aim to investigate the physical and chemical characteristic of RCA that influenced adsorption of P. RCA was analyzed using Scanning Electron Microscopy (SEM) and Energy-dispersive X-ray spectroscopy (EDX) testing to determine chemical composition. Results shows that RCA is highly contained with Aluminium, Calcium and Magnesium elements that enhanced the Phosphorus adsorption

MITOCHONDRIAL DNA POLYMORPHISMS AND FERTILITY IN BEEF CATTLE

Two regions of mitochondrial DNA, D-loop and ND-5 were characterized using polymerase chain reaction – restriction fragment length polymorphism (PCR-RFLP) involving 422 beef cattle of Hereford and composite breeds from Wokalup’s research station. ANOVA models (model I, II) were used to estimate associations between molecular haplotypes and quantitative traits. The phenotypic data used were records on calving rate, defined as the mean number of live calves born over four years, while the genotypic data used were the result of PCR-RFLP analysis in both regions of mitochondrial DNA using 7 restriction enzymes. The results of the present study have provided evidence that mitochondrial polymorphisms in the D-loop and ND-5 regions are associated significantly with fertility. This is the first report of a correlation between mitochondrial polymorphism in D-loop and ND-5 on fertility in beef cattle. Key words: PCR-RFLP, bovine mitochondrial DNA, D-loop, ND-5

Categorical characterizations of the natural numbers require primitive recursion

Simpson and the second author asked whether there exists a characterization of the natural numbers by a second-order sentence which is provably categorical in the theory RCA$^*_0$. We answer in the negative, showing that for any characterization of the natural numbers which is provably true in WKL$^*_0$, the categoricity theorem implies $\Sigma^0_1$ induction. On the other hand, we show that RCA$^*_0$ does make it possible to characterize the natural numbers categorically by means of a set of second-order sentences. We also show that a certain $\Pi^1_2$-conservative extension of RCA$^*_0$ admits a provably categorical single-sentence characterization of the naturals, but each such characterization has to be inconsistent with WKL$^*_0$+superexp.Comment: 17 page

Simulation, modelling and development of the metris RCA

In partnership with Metris UK we discuss the utilisation of modelling and simulation methods in the development of a revolutionary 7-axis Robot CMM Arm (RCA). An offline virtual model is described, facilitating pre-emptive collision avoidance and assessment of optimal placement of the RCA relative to scan specimens. Workspace accessibility of the RCA is examined under a range of geometrical assumptions and we discuss the effects of arbitrary offsets resulting from manufacturing tolerances. Degeneracy is identified in the number of ways a given pose may be attained and it is demonstrated how a simplified model may be exploited to solve the inverse kinematics problem of finding the “correct” set of joint angles. We demonstrate how the seventh axis may be utilised to avoid obstacles or otherwise awkward poses, giving the unit greater dexterity than traditional CMMs. The results of finite element analysis and static force modelling on the RCA are presented which provide an estimate of the forces exerted on the internal measurement arm in a range of poses

Revealing Comparative Advantage: Chaotic or Coherent Patterns Across Time and Sector and U.S. Trading Partner?

We map United States comparative advantage between 1980 and 1995, by trading partner and region, using Balassa's export-based index of Revealed Comparative Advantage (RCA). We find: temporally stable and ubiquitous US comparative advantage in differentiated producer goods (except disadvantage in Japan); somewhat less stable and less sweeping US disadvantage in standardized producer goods; chaotic and diverse patterns of US RCA in consumer goods (especially in the Chinese market). Our most significant findings are surprisingly sharp geographical differences in patterns of US RCA and surprisingly small differences across sub-sectors of 1, 2, and 3-digit SITC classifications - regional, but not sectoral, niche' specialization. The high overall variability across regions in RCA indexes seems unrelated to obvious explanations such as proximity or lingual/historical ties to the US. In producer goods, RCA variability across regions correlates somewhat better with accounts of trade diversion and of regional preferences for and discrimination against US exports. We find only scant evidence of high or increasing variability across disaggregated commodity sub-groups in US RCA indexes. Such variability is often the prediction of theories of comparative advantage that are based on vertical specialization, product differentiation, or scale and agglomeration economies.