Variations in leaf photosynthetic, morphological and biochemical properties with increasing plant height from seedlings to emergent trees were investigated in five dipterocarp species in a Malaysian tropical rain forest. Canopy openness increased significantly with tree height. Photosynthetic properties, such as photosynthetic capacity at light saturation, light compensation point, maximum rate of carboxylation and maximum rate of photosynthetic electron transport, all increased significantly with tree height. Leaf morphological and biochemical traits, such as leaf mass per area, palisade layer thickness, nitrogen concentration per unit area, chlorophyll concentration per unit dry mass and chlorophyll to nitrogen ratio, also changed significantly with tree height. Leaf properties had simple and significant relationships with tree height, with few intra- and interspecies differences. Our results therefore suggest that the photosynthetic capacity of dipterocarp trees depends on tree height, and that the trees adapt to the light environment by adjusting their leaf morphological and biochemical properties. These results should aid in developing models that can accurately estimate carbon dioxide flux and biomass production in tropical rain forests.
Polybrominated diphenyl ethers (PBDEs) are extensively used as flame retardants in many consumer products, and leachates from landfills have been identified as one of the possible sources of PBDEs in the environment. Meanwhile, the unprecedented economic and population growths of some Asian countries over the last decade have led to significant increases in the amount of waste containing PBDEs in that region. This study investigates the status of PBDEs in leachates from municipal solid waste dumping sites (MSWDS) in tropical Asian countries. A total of 46 PBDE congeners were measured, both in the adsorbed (n=24) and dissolved (n=16) phases, in leachate samples collected, from 2002 to 2010, from ten MSWDS distributed among the eight countries of Lao PDR, Cambodia, Vietnam, India, Indonesia, Thailand, the Philippines, and Malaysia. PBDEs were predominantly found in the adsorbed phase. Partitioning of PBDEs in the dissolved phase was associated with the presence of dissolved organic matter; the apparent organic carbon-normalized partition coefficients (K'oc) of the BDE congeners were lower by two to four orders of magnitude than the K oc predicted from the octanol-water partition coefficients (K ow). The total PBDE concentrations from mono- to deca-BDEs ranged from 3.7 to 133,000 ng/L, and showed a trend toward higher concentrations in the more populous and industrialized Asian countries. The congener profiles in the leachates basically reflected the composition of PBDE technical mixtures. The occurrence of congeners not contained, or in trace concentrations, in technical products (e.g., BDEs 208, 207, 206, 202, 188, 179, 49, 17/25, 8, 1) was observed in most of the leachate samples, suggesting the debromination of technical mixtures, including BDE-209, in the MSWDS of tropical Asian countries. Moreover, the temporal trend indicated the reduction of BDE-209 over time, with a corresponding increase in and/or emergence of lower brominated PBDE congeners. The results indicated that MSWDS of tropical Asian countries are potential sources of environmental PBDEs, which may be transported to the aquatic environment via dissolution with dissolved organic matter. MSWDS could be amplifiers of PBDE toxicity in the environment, possibly through debromination.
Photosynthetic rate, nitrogen concentration and morphological properties of canopy leaves were studied in 18 trees, comprising five dipterocarp species, in a tropical rain forest in Sarawak, Malaysia. Photosynthetic rate at light saturation (Pmax) differed significantly across species, varying from 7 to 18 micro mol m(-2) s(-1). Leaf nitrogen concentration and morphological properties, such as leaf blade and palisade layer thickness, leaf mass per area (LMA) and surface area of mesophyll cells per unit leaf area (Ames/A), also varied significantly across species. Among the relationships with leaf characteristics, Pmax had the strongest correlation with leaf mesophyll parameters, such as palisade cell layer thickness (r2 = 0.76, P < 0.001) and Ames/A (r2 = 0.73, P < 0.001). Leaf nitrogen concentration and Pmax per unit area also had a significant but weaker correlation (r2 = 0.46, P < 0.01), whereas Pmax had no correlation, or only weakly significant correlations, with leaf blade thickness and LMA. Shorea beccariana Burck, which had the highest P(max) of the species studied, also had the thickest palisade layer, with up to five or more layers. We conclude that interspecific variation in photosynthetic capacity in tropical rain forest canopies is influenced more by leaf mesophyll structure than by leaf thickness, LMA or leaf nitrogen concentration.
Seven sulfonamides, trimethoprim, five macrolides, lincomycin and three tetracyclines were measured in 150 water samples of sewage, livestock and aquaculture wastewater, and river and coastal waters, in five tropical Asian countries. The sum of the concentrations of the target antibiotics in sewage and heavily sewage-impacted waters were at sub- to low-ppb levels. The most abundant antibiotic was sulfamethoxazole (SMX), followed by lincomycin and sulfathiazole. The average concentration of SMX in sewage or heavily sewage-impacted waters was 1720 ng/L in Vietnam (Hanoi, Ho Chi Minh, Can Tho; n=15), 802ng/L in the Philippines (Manila; n=4), 538 ng/L in India (Kolkata; n=4), 282 ng/L in Indonesia (Jakarta; n=10), and 76 ng/L in Malaysia (Kuala Lumpur; n=6). These concentrations were higher than those in Japan, China, Europe, the US and Canada. A predominance of sulfonamides, especially SMX, is notable in these tropical countries. The higher average concentrations, and the predominance of SMX, can be ascribed to the lower cost of the antibiotics. Both the concentration and composition of antibiotics in livestock and aquaculture wastewater varied widely. In many cases, sulfamethazine (SMT), oxytetracycline (OTC), lincomycin, and SMX were predominant in livestock and aquaculture wastewater. Both human and animal antibiotics were widely distributed in the respective receiving waters (i.e., the Mekong River and Manila Bay). SMT/SMX ratios indicate a significant contribution from livestock wastewater to the Mekong River and nearby canals, with an estimated ~10% of river water SMX derived from such wastewater. Mass flow calculations estimate that 12 tons of SMX is discharged annually from the Mekong River into the South China Sea. Riverine inputs of antibiotics may significantly increase the concentration of such antibiotics in the coastal waters.
Many algorithms to detect copy number variations (CNVs) using exome sequencing (ES) data have been reported and evaluated on their sensitivity and specificity, reproducibility, and precision. However, operational optimization of such algorithms for a better performance has not been fully addressed. ES of 1199 samples including 763 patients with different disease profiles was performed. ES data were analyzed to detect CNVs by both the eXome Hidden Markov Model (XHMM) and modified Nord's method. To efficiently detect rare CNVs, we aimed to decrease sequencing biases by analyzing, at the same time, the data of all unrelated samples sequenced in the same flow cell as a batch, and to eliminate sex effects of X-linked CNVs by analyzing female and male sequences separately. We also applied several filtering steps for more efficient CNV selection. The average number of CNVs detected in one sample was <5. This optimization together with targeted CNV analysis by Nord's method identified pathogenic/likely pathogenic CNVs in 34 patients (4.5%, 34/763). In particular, among 142 patients with epilepsy, the current protocol detected clinically relevant CNVs in 19 (13.4%) patients, whereas the previous protocol identified them in only 14 (9.9%) patients. Thus, this batch-based XHMM analysis efficiently selected rare pathogenic CNVs in genetic diseases.