A note on the use of FTA™ technology for storage of blood samples for DNA analysis and removal of PCR inhibitors

peer-reviewedFTA™ technology is widely used across many molecular disciplines for sample capture, storage and analysis. The use of this technology for the long-term storage of blood samples for DNA analysis was examined as well as its potential to remove inhibitors from DNA samples previously extracted from blood with PCR inhibitors remaining. It was found that blood spots stored on FTA™ cards for 8 years at room temperature gave successful PCR products and that FTA™ cards are a useful tool for removing substances in samples which interfere with or inhibit, the PCR reaction

Investigation of Prolific Sheep from UK and Ireland for Evidence on Origin of the Mutations in BMP15 (FecXG, FecXB) and GDF9 (FecGH) in Belclare and Cambridge Sheep

peer-reviewedThis paper concerns the likely origin of three mutations with large effects on ovulation rate identified in the Belclare and Cambridge sheep breeds; two in the BMP15 gene (FecXG and FecXB) and the third (FecGH) in GDF9. All three mutations segregate in Belclare sheep while one, FecXB, has not been found in the Cambridge. Both Belclare and Cambridge breeds are relatively recently developed composites that have common ancestry through the use of genetic material from the Finnish Landrace and Lleyn breeds. The development of both composites also involved major contributions from exceptionally prolific ewes screened from flocks in Ireland (Belclare) and Britain (Cambridge) during the 1960s. The objective of the current study was to establish the likely origin of the mutations (FecXG, FecXB and FecGH) through analysis of DNA from Finnish Landrace and Lleyn sheep, and Galway and Texel breeds which contributed to the development of the Belclare breed. Ewes with exceptionally high prolificacy (hyper-prolific ewes) in current flocks on Irish farms were identified to simulate the screening of ewes from Irish flocks in the 1960s. DNA was obtained from: prolific ewes in extant flocks of Lleyn sheep (n = 44) on the Lleyn peninsula in Wales; hyper-prolific ewes (n = 41); prolific Galway (n = 41) ewes; Finnish Landrace (n = 124) and Texel (n = 19) ewes. The FecXG mutation was identified in Lleyn but not in Finnish Landrace, Galway or Texel sheep; FecXB was only found among the hyper-prolific ewes. The FecGH mutation was identified in the sample of Lleyn sheep. It was concluded from these findings that the Lleyn breed was the most likely source of the FecXG and FecGH mutations in Belclare and Cambridge sheep and that the FecXB mutation came from the High Fertility line that was developed using prolific ewes selected from commercial flocks in Ireland in the 1960′s and subsequently used in the genesis of the Belclare.Financial support through the Teagasc Walsh Fellowship Scheme, Genesis Faraday SPARK award (Lleyn survey) and Science Foundation Ireland (07/SRC/B1156) is gratefully acknowledged

Response to Teladorsagia circumcincta infection in Scottish Blackface lambs with divergent phenotypes for nematode resistance

peer-reviewedThe objective of this study was to identify Scottish Blackface lambs that were at the extremes of the spectrum of resistance to gastrointestinal nematodes and characterise their response to an experimental nematode challenge. Lambs (n = 90) were monitored for faecal egg count (FEC) (2 samples from each of 2 independent natural infections). The most resistant (n = 10) and susceptible (n = 10) individuals were selected and challenged with 30,000 Teladorsagia circumcincta larvae (L3) at 9 months of age. Response to infection was monitored by measuring FEC, plasma pepsinogen, serum antibodies against nematode larval antigens and haematology profile, until necropsy at 71 days post infection. Worm burden, worm fecundity and the level of anti-nematode antibodies in abomasal mucosa were determined at necropsy. FEC was consistently higher in susceptible animals (P < 0.05), validating the selection method. Worm fecundity was significantly reduced in resistant animals (P = 0.03). There was also a significant correlation (r = 0.88; P < 0.001) between the number of adult worms and FEC at slaughter. There was no effect of phenotype (resistance/susceptibility) on plasma pepsinogen or on haematology profile. Phenotype had a significant effect on the level of anti-nematode IgA antibodies in serum (P < 0.01), reflecting a higher peak in resistant animals at day 7 post infection. It is concluded that significant variation in the response to gastrointestinal nematode challenge exists within the Scottish Blackface population with resistant animals displaying significantly lower FEC, lower worm fecundity and higher concentration of anti-nematode IgA antibodies in serum.Kathryn McRae was supported by a Teagasc Walsh fellowship and the Allan and Grace Kay Overseas Scholarship

Rapid acquisition of wideline MAS solid-state NMR spectra with fast MAS, proton detection, and dipolar HMQC pulse sequences

The solid-state NMR spectra of many NMR active elements are often extremely broad due to the presence of chemical shift anisotropy (CSA) and/or the quadrupolar interaction (for nuclei with spin I \u3e 1/2). These NMR interactions often give rise to wideline solid-state NMR spectra which can span hundreds of kHz or several MHz. Here we demonstrate that by using fast MAS, proton detection and dipolar hetero-nuclear multiple-quantum (D-HMQC) pulse sequences, it is possible to rapidly acquire 2D spectra which correlate 1H chemical shifts to the indirectly detected wideline MAS powder patterns of dipolar coupled hetero-nuclei. The D-HMQC pulse sequence enables broadband excitation of the wideline hetero-nuclear NMR spectrum and provides higher sensitivity by detecting the narrower and more sensitive 1H NMR signal. This approach is demonstrated for the rapid acquisition of 2D 1H detected 195Pt solid-state NMR spectra of cisplatin and transplatin and the 71Ga solid-state NMR spectrum of a self-assembled Ga coordination polymer of unconfirmed structure. This approach should be broadly applicable for the rapid acquisition of wideline MAS solid-state NMR spectra of moderately abundant NMR nuclei

Understanding the efficiency of GPU algorithms for matrix-matrix multiplication

Utilizing graphics hardware for general purpose numerical computations has become a topic of considerable interest. The implementation of streaming algorithms, typified by highly parallel computations with little reuse of input data, has been widely explored on GPUs. We relax the streaming model&apos;s constraint on input reuse and perform an in-depth analysis of dense matrix-matrix multiplication, which reuses each element of input matrices O(n) times. Its regular data access pattern and highly parallel computational requirements suggest matrix-matrix multiplication as an obvious candidate for efficient evaluation on GPUs but, surprisingly we find even nearoptimal GPU implementations are pronouncedly less efficient than current cache-aware CPU approaches. We find the key cause of this inefficiency is that the GPU can fetch less data and yet execute more arithmetic operations per clock than the CPU when both are operating out of their closest caches. The lack of high bandwidth access to cached data will impair the performance of GPU implementations of any computation featuring significant input reuse

Sensitivity-Enhanced 207Pb Solid-State NMR Spectroscopy for the Rapid, Non-Destructive Characterization of Organolead Halide Perovskites

Organolead halide and mixed halide perovskites (CH3NH3PbX3, CH3NH3PbX3–nYn, X and Y = Cl–, Br– or I–), are promising materials for photovoltaics and optoelectronic devices. 207Pb solid-state NMR spectroscopy has previously been applied to characterize phase segregation and halide ion speciation in mixed halide perovskites. However, NMR spectroscopy is an insensitive technique that often requires large sample volumes and long signal averaging periods. This is especially true for mixed halide perovskites, which give rise to extremely broad 207Pb solid-state NMR spectra. Here, we quantitatively compare the sensitivity of the various solid-state NMR techniques on pure and mixed halide organolead perovskites and demonstrate that both fast MAS and DNP can provide substantial gains in NMR sensitivity for these materials. With fast MAS and proton detection, high signal-to-noise ratio two-dimensional (2D) 207Pb-1H heteronuclear correlation (HETCOR) NMR spectra can be acquired in less than half an hour from only ca. 5 µL of perovskite material. Modest relayed DNP enhancements on the order of 1 to 20 were obtained for perovskites. The cryogenic temperatures (110 K) used for DNP experiments also provide a significant boost in sensitivity. Consequently, it was possible to obtain the 207Pb solid-state NMR spectrum of a 300 nm thick model thin film of CH3NH3PbI3 in 34 hours by performing solid-state NMR experiments with a sample temperature of 110 K. This result demonstrates the possibility of using NMR spectroscopy for characterization of perovskite thin films