Aquaculture production in areas with high seasonal temperature variations: Development of planning tools

Postprint (published version)

Copy number variations of colorectal cancer by whole exome sequencing data

Colorectal cancer (CRC) is the third most common cancer and the fourth leading cause of cancer death worldwide. About 85% of the cases of CRC are known to have chromosomal instability, an allelic imbalance at several chromosomal loci, and chromosome amplification and translocation. The aim of this study is to determine the recurrent copy number variant (CNV) regions present in stage II of CRC through whole exome sequencing, a rapidly developing targeted next-generation sequencing (NGS) technology that provides an accurate alternative approach for accessing genomic variations. 42 normal-tumor paired samples were sequenced by Illumina Genome Analyzer. Data was analyzed with Varscan2 and segmentation was performed with R package R-GADA. Summary of the segments across all samples was performed and the result was overlapped with DEG data of the same samples from a previous study in the group1. Major and more recurrent segments of CNV were: gain of chromosome 7pq(13%), 13q(31%) and 20q(75%) and loss of 8p(25%), 17p(23%), and 18pq(27%). This results are coincident with the known literature of CNV in CRC or other cancers, but our methodology should be validated by array comparative genomic hybridisation (aCGH) profiling, which is currently the gold standard for genetic diagnosis of CNV.

Does soil moisture overrule temperature dependence of soil respiration in Mediterranean riparian forests?

Soil respiration (SR) is a major component of ecosystems' carbon cycles and represents the second largest CO2 flux in the terrestrial biosphere. Soil temperature is considered to be the primary abiotic control on SR, whereas soil moisture is the secondary control factor. However, soil moisture can become the dominant control on SR in very wet or dry conditions. Determining the trigger that makes soil moisture as the primary control factor of SR will provide a deeper understanding on how SR changes under the projected future increase in droughts. Specific objectives of this study were (1) to investigate the seasonal variations and the relationship between SR and both soil temperature and moisture in a Mediterranean riparian forest along a groundwater level gradient; (2) to determine soil moisture thresholds at which SR is controlled by soil moisture rather than by temperature; (3) to compare SR responses under different tree species present in a Mediterranean riparian forest (Alnus glutinosa, Populus nigra and Fraxinus excelsior). Results showed that the heterotrophic soil respiration rate, groundwater level and 30 cm integral soil moisture (SM30) decreased significantly from the riverside moving uphill and showed a pronounced seasonality. SR rates showed significant differences between tree species, with higher SR for P. nigra and lower SR for A. glutinosa. The lower threshold of soil moisture was 20 and 17% for heterotrophic and total SR, respectively. Daily mean SR rate was positively correlated with soil temperature when soil moisture exceeded the threshold, with Q10 values ranging from 1.19 to 2.14; nevertheless, SR became decoupled from soil temperature when soil moisture dropped below these thresholds.