A Comparison of Collection Techniques for Gene Expression Analysis of Human Oral Taste Tissue

Variability in human taste perception is associated with both genetic and environmental factors. The influence of taste receptor expression on this variability is unknown, in part, due to the difficulty in obtaining human oral tissue that enables quantitative expression measures of taste genes. In a comparison of six current techniques (Oragene RNeasy Kit, Isohelix swab, Livibrush cytobrush, tongue saliva, cheek saliva collection, and fungiform papillae biopsy), we identify the fungiform papillae biopsy is the optimal sampling technique to analyse human taste gene expression. The fungiform papillae biopsy resulted in the highest RNA integrity, enabling amplification of all the assessed taste receptor genes (TAS1R1, TAS1R2, TAS1R3, SCNN1A and CD36) and taste tissue marker genes (NCAM1, GNAT3 and PLCβ2). Furthermore, quantitative expression was observed in a subset of taste genes assessed from the saliva collection techniques (cheek saliva, tongue saliva and Oragene RNA kit). These saliva collection techniques may be useful as a non-invasive alternative sampling technique to the fungiform papillae biopsy. Identification of the fungiform papillae biopsy as the optimal collection method will facilitate further research into understanding the effect of gene expression on variability in human taste perception.     

Simulation of the potential distribution of rare and endangered Satyrium species in China under climate change

Satyrium is an endangered and rare genus of plant that has various pharmacodynamic functions. In this study, optimized MaxEnt models were used in analyzing potential geographical distributions under current and future climatic conditions (the 2050s and 2070s) and dominant environmental variables influencing their geographic distribution. The results provided reference for implementation of long‐term conservation and management approaches for the species. The results showed that the area of the total suitable habitat for Satyrium ciliatum (S. ciliatum) in China is 32.51 × 10⁴ km², the total suitable habitat area for Satyrium nepalense (S. nepalense) in China is 61.76 × 10⁴ km², and the area of the total suitable habitat for Satyrium yunnanense (S. yunnanense) in China is 89.73 × 10⁴ km² under current climatic conditions. The potential suitable habitat of Satyrium is mainly distributed in Southwest China. The major environmental variables influencing the geographical distribution of S. ciliatum were isothermality (bio3), temperature seasonality (bio4), and mean temperature of coldest quarter (bio11). Environmental variables such as isothermality (bio3), temperature seasonality (bio4), and precipitation of coldest quarter (bio19) affected the geographical distribution of S. nepalense; and environmental variables such as isothermality (bio3), temperature seasonality (bio4), and lower temperature of coldest month (bio6) affected the geographical distribution of S. yunnanense. The distribution range of Satyrium was extended as global warming increased, showing emissions of greenhouse gases with lower concentration (SSP1‐2.6) and higher concentration (SSP5‐8.5). According to the study, the distribution of suitable habitat will shift with a change to higher elevation areas and higher latitude areas in the future.     

Comparative genomics of koala,cattle and sheep strains of Chlamydia pecorum

Background

Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koalas. The genome of the C. pecorum VR629 (IPA) strain, isolated from a sheep with polyarthritis, was also sequenced.

Results

Comparisons of the draft C. pecorum genomes against the complete genomes of livestock C. pecorum isolates revealed that these strains have a conserved gene content and order, sharing a nucleotide sequence similarity > 98%. Single nucleotide polymorphisms (SNPs) appear to be key factors in understanding the adaptive process. Two regions of the chromosome were found to be accumulating a large number of SNPs within the koala strains. These regions include the Chlamydia plasticity zone, which contains two cytotoxin genes (toxA and toxB), and a 77 kbp region that codes for putative type III effector proteins. In one koala strain (MC/MarsBar), the toxB gene was truncated by a premature stop codon but is full-length in IPTaLE and DBDeUG. Another five pseudogenes were also identified, two unique to the urogenital strains C. pecorum MC/MarsBar and C. pecorum DBDeUG, respectively, while three were unique to the koala C. pecorum conjunctival isolate IPTaLE. An examination of the distribution of these pseudogenes in C. pecorum strains from a variety of koala populations, alongside a number of sheep and cattle C. pecorum positive samples from Australian livestock, confirmed the presence of four predicted pseudogenes in koala C. pecorum clinical samples. Consistent with our genomics analyses, none of these pseudogenes were observed in the livestock C. pecorum samples examined. Interestingly, three SNPs resulting in pseudogenes identified in the IPTaLE isolate were not found in any other C. pecorum strain analysed, raising questions over the origin of these point mutations.

Conclusions

The genomic data revealed that variation between C. pecorum strains were mainly due to the accumulation of SNPs, some of which cause gene inactivation. The identification of these genetic differences will provide the basis for further studies to understand the biology and evolution of this important animal pathogen.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-667) contains supplementary material, which is available to authorized users.     

Regression of diet-induced atherosclerosis in G?ttingen miniature swine

The regression of diet-induced atherosclerosis in G?ttingen Miniature Swine was investigated after a 6-month induction period. At 1 month after feeding a high-cholesterol and high-fat diet, levels of beta-lipoprotein, total cholesterol, free fatty acids and phospholipid had increased rapidly and the high levels were maintained throughout the 6 month induction period. Morphological features at 6 months showed fatty streaks in the thoracic aorta and fibrous plaques in the abdominal aorta. After return to the conventional diet at 6 months, serum lipids decreased rapidly and maintained the baseline level throughout the 9 month regression period. Histopathological findings showed the regression of fatty streaks but the fibrous plaques did not regress. The present study therefore confirms the regression of fatty streaks in the aorta of G?ttingen Miniature Swine by the administration of a cholesterol lowering diet.     

Decadal-scale rebuilding of predator biomass in Philippine marine reserves

No-take marine reserves (NTMRs) provide hope that local carrying capacity may be partially restored if reserves are protected long enough. How long is long enough? We assess the duration of protection required for populations of large predatory reef fish in marine reserves to attain new steady states. We monitored biomass of large predatory fish in two marine reserves at Sumilon and Apo Islands, Philippines, almost annually for 26 years (1983–2009), and fit a logistic model to the data. As duration of reserve protection increased, biomass of predatory fish approached an asymptote, although the models suggest that 20–40 years of protection is required to attain new steady states. Thus, for local carrying capacity to be rebuilt, no-take protection must be effective on decadal timescales.     

Chloroviruses encode a bifunctional dCMP-dCTP deaminase that produces two key intermediates in dTTP formation

The chlorovirus PBCV-1, like many large double-stranded DNA-containing viruses, contains several genes that encode putative proteins involved in nucleotide biosynthesis. This report describes the characterization of the PBCV-1 dCMP deaminase, which produces dUMP, a key intermediate in the synthesis of dTTP. As predicted, the recombinant protein has dCMP deaminase activity that is activated by dCTP and inhibited by dTTP. Unexpectedly, however, the viral enzyme also has dCTP deaminase activity, producing dUTP. Typically, these two reactions are catalyzed by proteins in separate enzyme classes; to our knowledge, this is the first example of a protein having both deaminase activities. Kinetic experiments established that (i) the PBCV-1 enzyme has a higher affinity for dCTP than for dCMP, (ii) dCTP serves as a positive heterotropic effector for the dCMP deaminase activity and a positive homotropic effector for the dCTP deaminase activity, and (iii) the enzymatic efficiency of the dCMP deaminase activity is about four times higher than that of the dCTP deaminase activity. Inhibitor studies suggest that the same active site is involved in both dCMP and dCTP deaminations. The discovery that the PBCV-1 dCMP deaminase has two activities, together with a previous report that the virus also encodes a functional dUTP triphosphatase (Y. Zhang, H. Moriyama, K. Homma, and J. L. Van Etten, J. Virol. 79:9945-9953, 2005), means that PBCV-1 is the first virus to encode enzymes involved in all three known pathways to form dUMP.     

Observations of poor swimming performance among hatchery-reared rainbow trout,Salmo gairdneri

Synopsis The swimming performance, as judged by maximum sustained swimming speed, of rainbow trout from a fish farm in S.W. England, is low when compared to previously published values for this species. This may be a localised peculiarity resulting from hatchery selection and rearing procedures.