Micro‐scale structure in the chemistry and biology of a shallow lake

1. Repeat sampling in daytime within a lily (Nuphar lutea) bed and in open water showed distinct heterogeneities in the three‐dimensional distributions of water chemistry and planktonic organisms on centimetre to decimetre scales. 2. Vertical gradients of physico‐chemical variables that did not exist at dawn developed during the day in both sites, as available nutrients were released from the sediments and were consumed towards the surface. 3. Distributions of algal standing crop suggest limitation by both nutrients and grazing. 4. Marked variability in distributions may question the assumptions often made about the homogeneity of plankton and available nutrient distributions in open water and in macrophyte stands of shallow lakes. Although simple sampling regimes for monitoring of water quality may be adequate for many purposes, they miss a fine structure in the water that is inherently interesting in understanding the underlying processes of plankton function.     

NLRC3 inhibits MCT-induced pulmonary hypertension in rats via attenuating PI3K activation

Phosphoinositide 3-kinase (PI3K) activation plays a critical role in the pulmonary vascular remodeling of pulmonary hypertension (PH). The nucleotide-oligomerization domain (NOD)-like receptor subfamily C3 (NLRC3) inhibits proliferation and inflammation via PI3K signaling in cancer. We previously showed NLRC3 was significantly reduced in PH patients, but the mechanism of function remains unclear. This study aimed to determine the potential role of NLRC3 in PH. We found that NLRC3 was downregulated in the pulmonary arteries of PH animal models and platelet-derived growth factor-BB (PDGF-BB) stimulated pulmonary arterial smooth muscle cells (PASMCs). NLRC3 pretreatment reduced right ventricular systolic pressure, attenuated pulmonary vascular remodeling and RVHI, and ameliorated proliferation, migration, and inflammation. Monocrotaline (MCT)- and PDGF-BB-mediated PI3K activation were suppressed by NLRC3 pretreatment. 740Y-P decreased the effect of NLRC3. Collectively, NLRC3 protected against MCT-induced rat PH and PDGF-BB-induced PASMC proliferation, migration, and inflammation through a mechanism involving PI3K inhibition. NLRC3 may have a therapeutic effect on PH and provide a promising therapeutic strategy for PH.     

Interaction of estrogen receptor β5 and interleukin 6 receptor in the progression of non–small cell lung cancer

Numerous studies have shown that the estrogen receptor beta (ERβ) and interleukin 6 receptor (IL-6R) had interaction in many tumors, including lung cancer. Previous studies found that ERβ5 exhibits a different biological function compared with the other subtypes of ERβ. Therefore, this study mainly explores the interaction between ERβ5 and IL-6R in the progression of lung cancer. We found that the expression of ERβ5, IL-6 and glycoprotein 130 (GP130) were significantly increased (P < 0.001) and the 5-year survival rate with the co-expression of ERβ5 and GP130 is significantly lower (P = 0.0315) in non-small cell lung cancer (NSCLC) patients. The cell proliferation, invasion, and cell cycle were markedly increased, and the cell apoptotic was markedly inhibited with the concurrent action of ERβ5 and IL-6 in A549 cells (P < 0.05). In addition, the expression of ERβ5, GP130, p-AKT, and p-44/42 MAPK was also significantly increased in A549 cells (P < 0.05). These results indicate that ERβ5 and GP130 can synergistically promote the progression of NSCLC and maybe combined as an independent prognostic factor in patients. In addition, these results also provide a theoretical basis for the combined targeting therapy of ERβ5 and GP130 in NSCLC.     

Stereological and gene expression examinations on the combined effects of photobiomodulation and curcumin on wound healing in type one diabetic rats

We examined the effects of photobiomodulation (PBM) independently and combined with curcumin on stereological parameters and basic fibroblast growth factor (bFGF), hypoxia-inducible factor-1α (HIF-1α), and stromal cell-derived factor-1α (SDF-1α) gene expressions in an excisional wound model of rats with type one diabetes mellitus (T1DM). T1DM was induced by an injection of streptozotocin (STZ) in each of the 90 male Wistar rats. One round excision was generated in the skin on the back of each of the 108 rats. The rats were divided into six groups (n = 18 per group): control (diabetic), untreated group; vehicle (diabetic) group, which received sesame oil; PBM (diabetic) group; curcumin (diabetic) group; PBM + curcumin (diabetic) group; and a healthy control group. On days 4, 7, and 15, we conducted both stereological and quantitative real-time PCR (qRT-PCR) analyses. The PBM and PBM + curcumin groups had significantly better inflammatory response modulation in terms of macrophages (P < .01), neutrophils (P < .001), and increased fibroblast values compared with the other groups at day 4 (P < .001), day 7 (P < .01), and day 15 (P < .001). PBM treatment resulted in increased bFGF gene expression on days 4 (P < .001) and 7 (P < .001), and SDF-1α gene expression on day 4 (P < .001). The curcumin group had increased bFGF (P < .001) expression on day 4. Both the PBM and PBM + curcumin groups significantly increased wound healing by modulation of the inflammatory response, and increased fibroblast values and angiogenesis. The PBM group increased bFGF and SDF-1α according to stereological and gene expression analyses compared with the other groups. The PBM and PBM + curcumin groups significantly increased the skin injury repair process to more rapidly reach the proliferation phase of the wound healing in T1DM rats.     

Mating system,pollen and propagule dispersal,and spatial genetic structure in a high-density population of the mangrove tree Kandelia candel

Mangrove tree species form ecologically and economically important forests along the tropical and subtropical coastlines of the world. Although low intrapopulation genetic diversity and high interpopulation genetic differentiation have been detected in most mangrove tree species, no direct investigation of pollen and propagule dispersal through paternity and/or parentage analysis and spatial genetic structure within populations has been conducted. We surveyed the mating system, pollen and propagule dispersal, and spatial genetic structure in a natural population of Kandelia candel, one of the typical viviparous mangrove tree species, using nuclear and chloroplast microsatellite markers. High diversity and outcrossing rates were observed. Paternity and parentage analysis and modelling estimations revealed the presence of an extremely short-distance component of pollen and propagule dispersal (pollen: 15.2 ± 14.9 m (SD) by paternity analysis and 34.4 m by modelling; propagule: 9.4 ± 13.8 m (SD) by parentage analysis, and 18.6 m by modelling). Genetic structure was significant at short distances, and a clumped distribution of chloroplast microsatellite genotypes was seen in K. candel adults. We conclude that the K. candel population was initiated by limited propagule founders from outside by long-distance dispersal followed by limited propagule dispersal from the founders, resulting in a half-sib family structure.     

First Description of Various Bacteria Resistant to Heavy Metals and Antibiotics Isolated from Polluted Sites in Tunisia

Environmental bacteria belonging to various families were isolated from polluted water collected from ten different sites in Tunisia. Sites were chosen near industrial and urban areas known for their high degree of pollution. The aim of this study was to investigate cross-resistance between heavy metals (HM), i.e., silver, mercury and copper (Ag, Hg, and Cu), and antibiotics. In an initial screening, 80 isolates were selected on ampicillin, and 39 isolates, retained for further analysis, could grow on a Tris-buffered mineral medium with gluconate as carbon source. Isolates were identified based on their 16S rRNA gene sequence. Results showed the prevalence of antibiotic resistance genes, especially all isolates harbored the bla_TEM gene. Some of them (15.38%) harbored bla_SHV. Moreover, several were even ESBLs and MBLs-producers, which can threaten the human health. On the other hand, 92.30%, 56.41%, and 51.28% of the isolates harbored the heavy metals resistance genes silE, cusA, and merA, respectively. These genes confer resistance to silver, copper, and mercury. A cross-resistance between antibiotics and heavy metals was detected in 97.43% of our isolates.     

CompareSVM: supervised,Support Vector Machine (SVM) inference of gene regularity networks

Background

Predication of gene regularity network (GRN) from expression data is a challenging task. There are many methods that have been developed to address this challenge ranging from supervised to unsupervised methods. Most promising methods are based on support vector machine (SVM). There is a need for comprehensive analysis on prediction accuracy of supervised method SVM using different kernels on different biological experimental conditions and network size.

Results

We developed a tool (CompareSVM) based on SVM to compare different kernel methods for inference of GRN. Using CompareSVM, we investigated and evaluated different SVM kernel methods on simulated datasets of microarray of different sizes in detail. The results obtained from CompareSVM showed that accuracy of inference method depends upon the nature of experimental condition and size of the network.

Conclusions

For network with nodes (<200) and average (over all sizes of networks), SVM Gaussian kernel outperform on knockout, knockdown, and multifactorial datasets compared to all the other inference methods. For network with large number of nodes (~500), choice of inference method depend upon nature of experimental condition. CompareSVM is available at http://bis.zju.edu.cn/CompareSVM/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0395-x) contains supplementary material, which is available to authorized users.