Copy Number Variation in Thai Population

Copy number variation (CNV) is a major genetic polymorphism contributing to genetic diversity and human evolution. Clinical application of CNVs for diagnostic purposes largely depends on sufficient population CNV data for accurate interpretation. CNVs from general population in currently available databases help classify CNVs of uncertain clinical significance, and benign CNVs. Earlier studies of CNV distribution in several populations worldwide showed that a significant fraction of CNVs are population specific. In this study, we characterized and analyzed CNVs in 3,017 unrelated Thai individuals genotyped with the Illumina Human610, Illumina HumanOmniexpress, or Illumina HapMap550v3 platform. We employed hidden Markov model and circular binary segmentation methods to identify CNVs, extracted 23,458 CNVs consistently identified by both algorithms, and cataloged these high confident CNVs into our publicly available Thai CNV database. Analysis of CNVs in the Thai population identified a median of eight autosomal CNVs per individual. Most CNVs (96.73%) did not overlap with any known chromosomal imbalance syndromes documented in the DECIPHER database. When compared with CNVs in the 11 HapMap3 populations, CNVs found in the Thai population shared several characteristics with CNVs characterized in HapMap3. Common CNVs in Thais had similar frequencies to those in the HapMap3 populations, and all high frequency CNVs (>20%) found in Thai individuals could also be identified in HapMap3. The majorities of CNVs discovered in the Thai population, however, were of low frequency, or uniquely identified in Thais. When performing hierarchical clustering using CNV frequencies, the CNV data were clustered into Africans, Europeans, and Asians, in line with the clustering performed with single nucleotide polymorphism (SNP) data. As CNV data are specific to origin of population, our population-specific reference database will serve as a valuable addition to the existing resources for the investigation of clinical significance of CNVs in Thais and related ethnicities.     

How adaptation and mass transfer control the biodegradation of linear alkylbenzene sulfonate by activated sludge

We use a nonsteady-state model to evaluate the effects of community adaptation and sorption kinetics on the fate of linear alkylbenzene sulfonate (LAS) in batch experiments conducted with activated sludge that was continuously fed different concentrations of LAS. We observed a sharp decrease in the biodegradation rate between 30 and 60 minutes and the presence of an LAS residual at the end of the batch experiments. The modeling analysis indicates that these phenomena were caused by relatively slow inter-phase mass transport of LAS. The modeling analyses also showed that the amount of LAS-degrading biomass increased when the continuous activated sludge was fed a higher LAS concentration. Although community adaptation to LAS involved accumulation of more LAS degraders, the increase was not proportional to the feed concentration of LAS, which supports the concept that LAS degraders also utilized portions of the general biochemical oxygen demand (BOD) fed to the continuous activated sludge systems.