Chromosome Three-Dimensional Structure Reconstruction: An Iterative ShRec3D Algorithm.

The three-dimensional (3D) structure of chromosomes is of great significance to ensure that the genome performs various functions (e.g., gene expression) correctly and replicates and separates correctly in mitosis. Since the emergence of Hi-C in 2009, a new experimental technique in molecular biology, researchers have been paying more and more attention to the reconstruction of chromosome 3D structure. To reconstruct the 3D structure of chromosomes based on Hi-C experimental data, many algorithms have been proposed, among which ShRec3D is one of the most outstanding. In this article, an iterative ShRec3D algorithm is presented to greatly improve the native ShRec3D algorithm. Experimental results show that our algorithm can significantly promote the performance of ShRec3D, and this improvement is applicable to almost all data noise range and signal coverage range, so it is universal.

Sample storage-induced changes in the quantity and quality of soil labile organic carbon.

Effects of sample storage methods on the quantity and quality of labile soil organic carbon are not fully understood even though their effects on basic soil properties have been extensively studied. We studied the effects of air-drying and frozen storage on cold and hot water soluble organic carbon (WSOC). Cold- and hot-WSOC in air-dried and frozen-stored soils were linearly correlated with those in fresh soils, indicating that storage proportionally altered the extractability of soil organic carbon. Air-drying but not frozen storage increased the concentrations of cold-WSOC and carbohydrate in cold-WSOC, while both increased polyphenol concentrations. In contrast, only polyphenol concentration in hot-WSOC was increased by air-drying and frozen storage, suggesting that hot-WSOC was less affected by sample storage. The biodegradability of cold- but not hot-WSOC was increased by air-drying, while both air-drying and frozen storage increased humification index and changed specific UV absorbance of both cold- and hot-WSOC, indicating shifts in the quality of soil WSOC. Our results suggest that storage methods affect the quantity and quality of WSOC but not comparisons between samples, frozen storage is better than air-drying if samples have to be stored, and storage should be avoided whenever possible when studying the quantity and quality of both cold- and hot-WSOC.

[Carbon density and production in valley spruce-fir forest in Xiaoxing'an Mountains, China].

The carbon density and production were measured using both forest inventory and allometry approaches in the declining valley spruce-fir forest in Xiaoxing' an Mountains. Results showed that the total carbon density of the forest was 268. 14 t C · hm(-2) in 2011, and carbon densities of the vegetation, detritus and soil were 74.25, 16.86 and 177.03 t C · hm(-2), respectively. From 2006 to 2011, tree layer carbon density decreased from 80.86 t C · hm(-2) to 71.73 t C · hm(-2). The average decrease proportions per year of carbon density were 0.5%, 1.2%, 2.7% and 3.7% for Abies nephrolepis, Betula platyphylla, Picea spp., and Larix gmelinii, respectively. However, carbon densities were increased by 2.9%, 3.9% and 7.2% per year for Alnus sibirica, Pinus koraiensis and Acer ukurunduense, respectively. Net primary production (NPP) of the forest was 4.69 t C · hm(-2) · a(-1). The ratio of belowground NPP to aboveground NPP was 0.56. Litterfall accounted for the largest proportion of the NPP of forest with a value of 34.5%. As the two most important carbon output approaches of forest ecosystems, the fluxes of heterotrophic respiration and coarse woody debris decomposition were 293.67 and 119.29 g C · m(-2) · a(-1), respectively. Net ecosystem production (NEP) of the forest was 55.90 g C · m(-2) a(-1). The results indicated that the valley spruce-fir forest in the declining state still had a certain carbon sink capacity.

[Effects of selective cutting on the carbon density and net primary productivity of a mixed broadleaved-Korean pine forest in Northeast China].

To accurately quantify forest carbon density and net primary productivity (NPP) is of great significance in estimating the role of forest ecosystems in global carbon cycle. By using the forest inventory and allometry approaches, this paper measured the carbon density and NPP of the virgin broadleaved-Korean pine (Pinus koraiensis) forest and of the broadleaved-Korean pine forest after 34 years selective-cutting (the cutting intensity was 30%, and the cutting trees were in large diameter class). The total carbon density of the virgin and selective-cutting broadleaved-Korean pine forests was (397.95 +/- 93.82) and (355.61 +/- 59.37) t C x hm(-2), respectively. In the virgin forest, the carbon density of the vegetation, debris, and soil accounted for 31.0%, 3.1%, and 65.9% of the total carbon pool, respectively; in the selective-cutting forest, the corresponding values were 31.7%, 2.9%, and 65.4%, respectively. No significant differences were observed in the total carbon density and the carbon density of each component between the two forests. The total NPP of the virgin and selective-cutting forests was (36.27 +/- 0.36) and (6.35 +/- 0.70) t C x hm(-2) x a(-1), among which, the NPP of overstory, understory, and fine roots in virgin forest and selective-cutting forest accounted for 60.3%, 2.0%, and 37.7%, and 66.1%, 2.0%, and 31.2%, respectively. No significant differences were observed in the total NPP and the contribution rate of each component between the two forests. However, the ratios of the needle and broadleaf NPPs of the virgin and selective-cutting forests were 47.24:52.76 and 20.48:79.52, respectively, with a significant difference. The results indicated that the carbon density and NPP of the broadleaved-Korean pine forest after 34 years selective-cutting recovered to the levels of the virgin broadleaved-Korean pine forest.