Prediction of effective genome size in metagenomic samples

We introduce a novel computational approach to predict effective genome size (EGS; a measure that includes multiple plasmid copies, inserted sequences, and associated phages and viruses) from short sequencing reads of environmental genomics (or metagenomics) projects. We observe considerable EGS differences between environments and link this with ecologic complexity as well as species composition (for instance, the presence of eukaryotes). For example, we estimate EGS in a complex, organism-dense farm soil sample at about 6.3 megabases (Mb) whereas that of the bacteria therein is only 4.7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects.     

Reptile responses to fire and the risk of post-disturbance sampling bias

Altered fire regimes are a driver of biodiversity decline. To plan effective management, we need to know how species are influenced by fire and to develop theory describing fire responses. Animal responses to fire are usually measured using methods that rely on animal activity, but animal activity may vary with time since fire, potentially biasing results. Using a novel approach for detecting bias in the pit-fall trap method, we found that leaf-litter dependent reptiles were more active up to 6 weeks after fire, giving a misleading impression of abundance. This effect was not discovered when modelling detectability with zero-inflated binomial models. Two species without detection bias showed early-successional responses to time since fire, consistent with a habitat-accommodation succession model. However, a habitat specialist did not have the predicted low abundance after fire due to increased post-fire movement and non-linear recovery of a key habitat component. Interactions between fire and other processes therefore must be better understood to predict reptile responses to changing fire-regimes. We conclude that there is substantial bias when trapping reptiles after fire, with species that are otherwise hard to detect appearing to be abundant. Studies that use a survey method based on animal activity such as bird calls or animal movements, likely face a similar risk of bias when comparing recently-disturbed with control sites.     

Involvement of regulatory volume decrease in the migration of nasopharyngeal carcinoma cells

The transwell chamber migration assay and CCD digital camera imaging techniques were used to investigate the relationship between regulatory volume decrease (RVD) and cell migration in nasopharyngeal carcinoma cells (CNE-2Z cells). Both migrated and non-migrated CNE-2Z cells, when swollen by 47% hypotonic solution, exhibited RVD which was inhibited by extracellular application of chloride channel blockers adenosine 5‘-triphosphate (ATP), 5-nitro-2-(3-phenylpropylamino) benzoic acid (NPPB) and tamoxifen. However, RVD rate in migrated CNE-2Z cells was bigger than that of non-migrated cells and the sensitivity of migrated cells to NPPB and tamoxifen was higher than that of nonmigrated cells. ATP, NPPB and tamoxifen also inhibited migration of CNE-2Z cells. The inhibition of migration was positively correlated to the blockage of RVD, with a correlation coefficient (r) = 0.99, suggesting a functional relationship between RVD and cell migration. We conclude that RVD is involved in cell migration and RVD may play an important role in migratory process in CNE-2Z cells.     

Associations between primates and other mammals in a central Amazonian forest landscape

Little information exists on mixed-species groups between primates and other mammals in Neotropical forests. In this paper, we describe three such associations observed during an extensive large-vertebrate survey in central Amazonia, Brazil. Mixed-species groups between a primate species and another mammal were observed on seven occasions between squirrel monkeys (Saimiri cf. ustus) and either South American coatis (Nasua nasua) or tayras (Eira barbara) and between brown capuchins (Cebus apella) and coatis. All associations were restricted to floodplain forest during its dry stage. We suggest that the associations involving the coatis are connected to foraging and vigilance but may be induced by a common alternative food resource at a time of food shortage.     

The chimeric cytokine Hyper-IL-6 enhances the efficiency of lentiviral gene transfer in hepatocytes both in vitro and in vivo

Lentiviral vectors have been used for gene transfer into the liver but their ability to efficiently transduce quiescent hepatocytes remains controversial. Lentivirus-mediated gene transfer is more efficient in cycling cells. We determine the effect of H-IL6 in the lentiviral transduction. The lentiviral vector was used to transduce HepG2 cells and mice liver cells, previously treated with H-IL6. The highest transduction level was observed in HepG2 cells treated with 30 ng/mL H-IL6 and in the mice that received 4 μg H-IL6. Our results suggest that H-IL6 is an inducer of lentiviral gene transfer into the liver cells without any toxicity.     

Combination of bone tissue engineering and BMP-2 gene transfection promotes bone healing in osteoporotic rats

OBJECTIVE: The aim of this study was to develop a feasible approach to promote bone healing in osteoporotic rats using autogenous bone tissue-engineering and gene transfection of human bone morphogenetic protein 2 (hBMP-2). METHODS: Bone marrow stromal cells (BMSCs) from the left tibia of osteoporotic rats were transfected with the hBMP-2 gene in vitro which was confirmed by immunohistochemistry, in situ hybridization and Western blotting. Autogenous transfected or untransfected BMSCs were seeded on macroporous coral hydroxyapatite (CHA) scaffolds. Each cell-scaffold construct was implanted into a defect site which was created in the ramus of the mandible of osteoporotic rats. Four or eight weeks after implantation in situ hybridization was performed in BMSCs transfected with hBMP-2, X-ray examinations, histological and histomorphological analyses were used to evaluate the effect of tissue-engineered bone on osseous defect repair. RESULTS: Newly formed bone was observed at the margin of the defect 4 weeks after implantation with BMSCs transfected with BMP-2. Mature bone was observed 8 weeks after treatment. In the control group there was considerably less new bone and some adipose tissue was observed at the defect margins 8 weeks after implantation. CONCLUSIONS: Autogenous cells transfected with hBMP-2 promote bone formation in osteoporotic rats. BMSC-mediated BMP-2 gene therapy used in conjunction with bone tissue engineering may be used to successfully treat bone defects in osteoporotic rats. This method provides a powerful tool for bone regeneration and other tissue engineering.     

Sortase-mediated protein ligation: an emerging biotechnology tool for protein modification and immobilisation

Sortases are transpeptidases produced by Gram-positive bacteria to anchor cell surface proteins covalently to the cell wall. The Staphylococcus aureus sortase A (SrtA) cleaves a short C-terminal recognition motif (LPXTG) on the target protein followed by the formation of an amide bond with the pentaglycine cross-bridge in the cell wall. Over recent years, several researchers have exploited this specific reaction for a range of biotechnology applications, including the incorporation of non-native peptides and non-peptidic molecules into proteins, the generation of nucleic acid–peptide conjugates and neoglycoconjugates, protein circularisation, and labelling of cell surface proteins on living cells.     

The effect of jasmonic acid on the accumulation of ABA,proline and spermidine and its influence on membrane injury under water deficit in two barley genotypes

Seedlings of two barley genotypes (‘Maresi’ and wild form of Hordeum spontaneum) were treated with jasmonic acid (JA 5 μM and 15 μM) for 24 h, and then subjected to water stress (PEG 6000 solution of − 1.5 MPa). JA caused an increase in the content of ABA but not in that of proline and spermidine in the two studied genotypes. The effect of the treatment did not depend on the applied JA concentration. The pre-stress treatment with JA changed plant response to water deficit with regard to membrane injury. Treatment with a lower JA concentration (5 μM) caused a substantial reduction of the stress-induced membrane damage in the both genotypes. A higher JA concentration (15 μM) caused the reduction of membrane injury only in H. spontaneum and was ineffective in ‘Maresi’. JA had no influence on the leaf water status in water-stressed plants. A possible role of JA in leaf ABA accumulation and alleviation of cell membrane injury under water deficit is discussed. The work was partly supported by the Polish Committee For Scientific Research, grant No 5 PO6A 036 18     

高血压病患者肠系膜动脉平滑肌细胞钙激活钾通道研究

目的:研究高血压病患者肠系膜动脉平滑肌细胞钙激活钾通道(KCa)的功能活动。方法:应用膜片钳制技术内面向外式单通道记录方法。结果:①人肠系膜动脉平滑肌细胞KCa开放具有电压依赖性。KCa通道电导在高血压组、正常组分别为191.4pS、197.7pS。胞内侧应用TEA可阻断通道。②增加浴液中Ca2 浓度(从0增至10-8、10-7、5×10-7、10-6mol/L),各组KCa开放概率(Po)均呈浓度依赖性增加,高血压组Po从0.016增至0.023、0.031、0.053、0.094,正常组Po从0.004增至0.023、0.041、0.072、0.184。通道平均开放时间延长,平均关闭时间缩短。③Ca2 浓度为0时,高血压组KCa开放概率明显高于正常组,在其它Ca2 浓度下高血压组KCa开放概率等于或低于正常组。结论:高血压病患者肠系膜动脉平滑肌细胞KCa的Ca2 敏感性较低,可能促进高血压的发生。