A particle swarm optimizer with passive congregation

This paper presents a particle swarm optimizer (PSO) with passive congregation to improve the performance of standard PSO (SPSO). Passive congregation is an important biological force preserving swarm integrity. By introducing passive congregation to PSO, information can be transferred among individuals of the swarm. A particle swarm optimizer with passive congregation (PSOPC) is tested with a set of 10 benchmark functions with 30 dimensions and compared to a global version of SPSO (GSPSO), a local version of SPSO (LSPSO), and PSO with a constriction factor (CPSO), respectively. Experimental results indicate that the PSO with passive congregation improves the search performance on the benchmark functions significantly.     

The role of zinc in caspase activation and apoptotic cell death

In addition to its diverse role in many physiological systems, zinc (Zn) has now been shown to be an important regulator of apoptosis. The purpose of this review is to integrate previously published knowledge on Zn and apoptosis with current attempts to elucidate the mechanisms of action of this biometal. This paper begins with an introduction to apoptosis and then briefly reviews the evidence relating Zn to apoptosis. The major focus of this review is the mechanistic actions of Zn and its candidate intracellular targets. In particular, we examine the cytoprotective functions of Zn which suppress major pathways leading to apoptosis, as well as the more direct influence of Zn on the apoptotic regulators, especially the caspase family of enzymes. These two mechanisms are closely related since a decline in intracellular Zn below a critical threshold level may not only trigger pathways leading to caspase activation but may also facilitate the process by which the caspases are activated. Studies by our laboratory in airway epithelial cells show that Zn is co-localized with the precursor form of caspase-3, mitochondria and microtubules, suggesting this Zn is critically placed to control apoptosis. Further understanding the different pools of Zn and how they interact with apoptotic pathways should have importance in human disease.     

Lysosomal trafficking functions of mucolipin-1 in murine macrophages

Background  

Mucolipidosis Type IV is currently characterized as a lysosomal storage disorder with defects that include corneal clouding, achlorhydria and psychomotor retardation. MCOLN1, the gene responsible for this disease, encodes the protein mucolipin-1 that belongs to the "Transient Receptor Potential" family of proteins and has been shown to function as a non-selective cation channel whose activity is modulated by pH. Two cell biological defects that have been described in MLIV fibroblasts are a hyperacidification of lysosomes and a delay in the exit of lipids from lysosomes.     

A Ubiquitin-Binding Domain that Binds a Structural Fold Distinct from that of Ubiquitin

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Fine-scale spatial genetic structure and gene flow in a small, fragmented population of Sinojackia rehderiana (Styracaceae), an endangered tree species endemic to China

Populations of Sinojackia rehderiana are highly threatened and have small and scattered distribution due to habitat fragmentation and human activities. Understanding changes in genetic diversity, the fine-scale spatial genetic structure (SGS) at different life stages and gene flow of S. rehderiana is critical for developing successful conservation strategies for fragmented populations of this endangered species. In this study, 208 adults, 114 juveniles and 136 seedlings in a 50 × 100-m transect within an old-growth forest were mapped and genotyped using eight microsatellite makers to investigate the genetic diversity and SGS of this species. No significant differences in genetic diversity among different life-history stages were found. However, a significant heterozygote deficiency in adults and seedlings may result from substantial biparental inbreeding. Significant fine-scale spatial structure was found in different life-history stages within 19 m, suggesting that seed dispersal mainly occurred near a mother tree. Both historical and contemporary estimates of gene flow (13.06 and 16.77 m) indicated short-distance gene dispersal in isolated populations of S. rehderiana. The consistent spatial structure revealed in different life stages is most likely the result of limited gene flow. Our results have important implications for conservation of extant populations of S. rehderiana. Measures for promoting pollen flow should be taken for in situ conservation. The presence of a SGS in fragmented populations implies that seeds for ex situ conservation should be collected from trees at least 19-m apart to reduce genetic similarity between neighbouring individuals.     

Integrated soil and plant phosphorus management for crop and environment in China. A review

In semi-arid grassland ecosystems, soil biogeochemical processes are controlled by seasonal and inter-annual rainfall variation and temperature, which may override the long-term impact of grazers on N availability and N dynamics. In a three-year (2004?C2006) case study of an Inner Mongolian grassland, we analysed time-integrated (ion-exchange resins) and instantaneous (soil mineral N extractions) inorganic N availability at three sites of varying grazing intensities and combined these data with information on soil water content (SWC), aboveground net primary productivity (ANPP) and plant N uptake. Additionally, the effects of rainfall and grazing on N-form availability (NO ₃ ^? -N, NH ₄ ⁺ -N) were considered. Grazing had less impact on N availability compared to seasonal and annual rainfall distribution. One of the three study years (2004) showed a grazing effect with higher resin-N availability at the ungrazed site compared to the heavily grazed site. Inorganic N availability was low in the driest year (2005) and highest in a year of average rainfall amount and favourable distribution (2004). In general, we found a positive relationship between inorganic N availability and both plant productivity and plant N uptake. Rainfall also controlled the plant available NO ₃ ^? -N and NH ₄ ⁺ -N pools; NH ₄ ⁺ -N dominated the available inorganic N-form in times of low SWC, while the available NO ₃ ^? -N increased with SWC. We observed N availability and plant productivity in a temporal synchronized pattern. Increased rainfall variability and land-use practices affecting SWC will likely alter N availability dynamics (and the relation of N-forms) and, therefore, important processes of semi-arid natural grassland carbon and N cycling.     

Phosphoinositide-dependent kinase 1–associated glycolysis is regulated by miR-409-3p in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most popular kidney cancer in adults. Metabolic shift toward aerobic glycolysis is a fundamental factor for ccRCC therapy. MicroRNAs (miRNAs) are thought to be important regulators in ccRCC development and progression. Phosphoinositide-dependent kinase 1 (PDK1) is required for metabolic activation; however, the role of PDK1-induced glycolytic metabolism regulated by miRNAs is unclear in ccRCC. So, the purpose of the current study is to elucidate the underlying mechanism in ccRCC cell metabolism mediated by PDK1. Our results revealed that miR-409-3p inhibited glycolysis by regulating PDK1 expression in ccRCC cells. We also found that miR-409-3p was regulated by hypoxia. Our results indicated that PDK1 facilitated ccRCC cell glycolysis, regulated by miR-409-3p in hypoxia.     

三疣梭子蟹卵巢发育过程中主要类胡萝卜素组成变化及其与抗氧化性能的关系

实验研究了三疣梭子蟹(Portunus trituberculatus)卵巢发育过程中(Ⅰ—V期)组织色泽、类胡萝卜素组成与含量、抗氧化和非特异性免疫指标的变化规律,进一步探讨了肝胰腺中类胡萝卜素含量变化与抗氧化指标的关系。结果表明:(1)卵巢发育期间,卵巢指数(GSI)显著增加(P<0.05),肝胰腺指数(HSI)整体呈先升后降的趋势;卵巢的红度(a*)值和黄度(b*)值、肝胰腺的亮度(L*)值和b*值均呈显著上升趋势,但卵巢中L*值呈下降趋势。(2)在卵巢发育过程中,卵巢中的总类胡萝卜素、虾青素、叶黄素和β-胡萝卜素含量均为先升后降的趋势,虾青素含量在Ⅳ期最高;肝胰腺中的虾青素含量呈上升趋势,而β-胡萝卜素含量为显著下降趋势;内表皮中的总类胡萝卜素、虾青素、叶黄素、海胆烯酮和β-胡萝卜素含量均呈现下降趋势;就不同组织中类胡萝卜素含量而言,内表皮中虾青素含量最高。卵巢和肝胰腺的L*值与总类胡萝卜素含量呈显著负相关,卵巢的a*值和b*值均与总类胡萝卜素、虾青素、叶黄素、海胆烯酮和β-胡萝卜素含量呈显著正相关。肝胰腺的a*值与各类胡萝卜素含量无显著相关性, b*值仅与虾青素含量呈显...     

果肉和埋土深度对新疆野杏种子萌发与幼苗生长的影响

为探明新疆野杏（Armeniaca vulgaris）种子萌发与幼苗生长对果肉和埋土深度的响应,以期为新疆野杏的天然更新与实生苗培育提供理论参考。通过2种果皮结构（有果肉和无果肉）的种子在不同埋土深度（地表至18.0 cm的14个梯度）对新疆野杏种子萌发和幼苗生长进行研究,旨在揭示果皮结构和埋土深度对新疆野杏种子萌发与成苗能力的影响。结果表明：果肉和埋土深度显著影响野杏种子的萌发、幼苗生长与质量（P<0.05）。埋土深度<3.0 cm不利于成苗,埋土深度>6.0 cm时,萌发能力与幼苗生长量随埋土深度的增加而降低,3.0～6.0cm为适宜埋土深度。无果肉种子萌发优于有果肉种子,萌发率、萌发指数、成苗率、活力指数分别增长了37.18%、3.88%、37.18%、26.59%,幼苗高、基径、叶片数量、根冠比、幼苗质量指数分别增长了36.99%、7.48%、68.69%、20.61%、14.29%,其萌发能力与幼苗生长量显著高于有果肉种子（P<0.05）。有无果肉种子的萌发和幼苗生长指标与埋土深度呈显著负相关（P<0.05）。研究结果表明,无果肉处理对新疆野杏种...     

Insular Organization of Gene Space in Grass Genomes

Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands “gene insulae” to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschii chromosomes is shown to be primarily caused by shortening of inter-insular distances. The comparison of the four grass genomes suggests that gene locations are largely a function of a homogeneous Poisson process in small genomes. Nonrandom insertions of LTR retroelements during genome expansion creates gene insulae, which become less dense and further apart with the increase in genome size. High concordance in relative lengths of orthologous intergenic distances among the investigated genomes including the maize genome suggests functional constraints on gene distribution in the grass genomes.