Bioaccumulation and Physiological Response of Five Willows to Toxic Levels of Cadmium and Zinc

We evaluated the phytoremediation potential of Salix spp. exposed to high cadmium (Cd) and zinc (Zn) concentrations to select feasible plant materials for restoration and revegetation of mining soil contaminated by heavy metals on the basis of their Cd and Zn accumulation, Cd-Zn interaction on bioaccumulation, and the changes of photosynthetic parameters. The Cd and Zn concentrations were in the order of root > leaf > stem, regardless of the species. In the combined Cd and Zn treatment, the leaf and stem Cd concentration in all species were higher relative to Cd-alone treatment. In contrast, the Zn concentration in plant tissues when exposed to the combined Cd + Zn treatment decreased relative to the Zn-alone treatment. The translocation factor (TF) of Cd and Zn from root to leaf was generally higher compared to TF from root to stem than those in the single treatment. The Cd + Zn treatments resulted in enhanced translocation of Cd from root to aboveground tissue (synergistic), while the same treatment suppressed the Zn translocation from root to leaf and stem (antagonistic). The reduction of photosynthetic parameters in Zn alone and Cd + Zn treatments was generally higher than that of Cd-alone treatment. Among the different species, S. caprea and P. alba×glandulosa have the lowest photosynthetic reduction relative to the control. Overall, S. caprea could be a potential candidate for phytoremediation of Cd- and Zn-contaminated sites.     

Cell-mediated Immune Response in Primary Biliary Cirrhosis to a Protein Fraction from Human Bile

Cell-mediated immune responses to a protein fraction of human bile have been demonstrated, using the leucocyte migration test, in eight out of 10 patients with primary biliary cirrhosis but in only three out of nine with active chronic hepatitis. In the latter condition sensitization to a liver-specific hepatocellular antigen was found more frequently (five out of nine patients) than in primary biliary cirrhosis (two out of 10). These results, as well as the granuloma formation observed histologically, suggest that the initial bile duct lesion in primary biliary cirrhosis may be associated with a cell-mediated response to antigens—perhaps derived from bile duct epithelial cells—which may be normal constituents of hepatic bile.     

Computational Modeling of Tumor Response to Drug Release from Vasculature-Bound Nanoparticles

Systemically injected nanoparticle (NPs) targeting tumor vasculature offer a venue for anti-angiogenic therapies as well as cancer detection and imaging. Clinical application has been limited, however, due to the challenge of elucidating the complex interplay of nanotechnology, drug, and tumor parameters. A critical factor representing the likelihood of endothelial adhesion is the NP vascular affinity, a function of vascular receptor expression and NP size and surface-bound ligand density. We propose a theoretical framework to simulate the tumor response to vasculature-bound drug-loaded NPs and examine the interplay between NP distribution and accumulation as a function of NP vascular affinity, size, and drug loading and release characteristics. The results show that uniform spatial distribution coupled with high vascular affinity is achievable for smaller NPs but not for larger sizes. Consequently, small (100 nm) NPs with high vascular affinity are predicted to be more effective than larger (1000 nm) NPs with similar affinity, even though small NPs have lower drug loading and local drug release compared to the larger NPs. Medium vascular affinity coupled with medium or larger sized NPs is also effective due to a more uniform distribution with higher drug loading and release. Low vascular affinity hampered treatment efficacy regardless of NP size, with larger NPs additionally impeded by heterogeneous distribution and drug release. The results further show that increased drug diffusivity mainly benefits heterogeneously distributed NPs, and would negatively affect efficacy otherwise due to increased wash-out. This model system enables evaluation of efficacy for vascular-targeted drug-loaded NPs as a function of critical NP, drug, and tumor parameters.     

DNA Damage Response: Three Levels of DNA Repair Regulation

Genome integrity is challenged by DNA damage from both endogenous and environmental sources. This damage must be repaired to allow both RNA and DNA polymerases to accurately read and duplicate the information in the genome. Multiple repair enzymes scan the DNA for problems, remove the offending damage, and restore the DNA duplex. These repair mechanisms are regulated by DNA damage response kinases including DNA-PKcs, ATM, and ATR that are activated at DNA lesions. These kinases improve the efficiency of DNA repair by phosphorylating repair proteins to modify their activities, by initiating a complex series of changes in the local chromatin structure near the damage site, and by altering the overall cellular environment to make it more conducive to repair. In this review, we focus on these three levels of regulation to illustrate how the DNA damage kinases promote efficient repair to maintain genome integrity and prevent disease.The DNA in each of our cells accumulates thousands of lesions every day. This damaged DNA must be removed for the DNA code to be read properly. Fortunately, cells contain multiple DNA repair mechanisms including: base excision repair (BER) that removes damaged bases, mismatch repair (MMR) that recognizes base incorporation errors and base damage, nucleotide excision repair (NER) that removes bulky DNA adducts, and cross-link repair (ICL) that removes interstrand cross-links. In addition, breaks in the DNA backbone are repaired via double-strand break (DSB) repair pathways including homologous recombination (HR) and nonhomologous end joining (NHEJ). Some of these mechanisms can operate independently to repair simple lesions. However, the repair of more complex lesions involving multiple DNA processing steps is regulated by the DNA damage response (DDR). For the most difficult to repair lesions, the DDR can be essential for successful repair.The DDR consists of multiple pathways, but for the purposes of this review we will focus on the DDR kinase signaling cascades controlled by the phosphatidylinositol 3-kinase-related kinases (PIKK). These kinases include DNA-dependent protein kinase (DNA-PKcs), ataxia telangiectasia-mutated (ATM), and ATM and Rad3-related (ATR). DNA-PKcs and ATM are primarily involved in DSB repair, whereas ATR responds to a wide range of DNA lesions, especially those associated with DNA replication (Cimprich and Cortez 2008). ATR’s versatility makes it essential for the viability of replicating cells in mice and humans (Brown and Baltimore 2000; de Klein et al. 2000; Cortez et al. 2001). In the case of ATM, inherited biallelic mutations cause ataxia-telangiectasia—a disorder characterized by neurodegeneration, immunodeficiency, and cancer (Shiloh 2003; Lavin 2008). ATM mutations are also frequently found in several types of tumors (Negrini et al. 2010).The DDR kinases share several common regulatory mechanisms of activation (Lovejoy and Cortez 2009). All three DDR kinases sense damage through protein–protein interactions that serve to recruit the kinases to damage sites. Once localized, posttranslational modifications and other protein–protein interactions fully activate the kinases to initate a cascade of phosphorylation events. The best-studied substrate of DNA-PKcs is actually DNA-PKcs itself, and autophosphorylation is an important step in direct religation of the DSB via nonhomologous end joining (NHEJ) (Weterings and Chen 2007; Dobbs et al. 2010). ATM and ATR have both unique and shared substrates that participate in DNA repair, checkpoint signaling, and determining cell fate decisions such as apoptosis and sensescence.     

The Extreme Variety of Genotoxic Response to Benzo[a]pyrene in Three Different Human Cell Lines from Three Different Organs

Polycyclic aromatic hydrocarbons (PAHs) are associated with occupational exposure and urban atmospheric pollution. Determination of the genotoxic properties of these compounds is thus of outmost importance. For this purpose a variety of cellular models have been widely used. Reliable results can however only be obtained with models reflecting the specific sensitivity of different organs towards PAHs. In this work, we compared the response to benzo[a]pyrene in cell lines from human lungs (A549) and bladder (T24); two important target organs for PAHs-induced cancer. Human hepatocytes (HepG2) were used as a reference, although liver is not a concern for PAHs carcinogenesis. Adducts arising from the ultimate diol-epoxide metabolite of B[a]P, BPDE, were found to be produced in a dose-dependent manner in HepG2. BPDE DNA adducts were not detected in T24 and in A549 their formation was found to be most efficient at the lowest concentration studied (0.2 µM). These results are probably explained by differences in induction and activity of phase I metabolization enzymes, as well as by proteins eliminating the B[a]P epoxide in A549. In addition to BPDE adducts, oxidative DNA damage, namely strand breaks and oxidized purines were measured and found to be produced only in minute amounts in all three cell lines. In summary, our results emphasize the large differences in the response of cells originating from different organs. Our data also point out the importance of carefully selecting the doses used in in vitro toxicological experiments. The example of A549 shows that working at high doses may lead to an underestimation of the risk. Finally, the choice of method for evaluating genotoxicity appears to be of crucial importance. The comet assay does not seem to be the best method for a compound like B[a]P which induces stable adducts causing limited oxidative damage.     

Development of a Three Dimensional Multiscale Computational Model of the Human Epidermis

Transforming Growth Factor (TGF-β1) is a member of the TGF-beta superfamily ligand-receptor network. and plays a crucial role in tissue regeneration. The extensive in vitro and in vivo experimental literature describing its actions nevertheless describe an apparent paradox in that during re-epithelialisation it acts as proliferation inhibitor for keratinocytes. The majority of biological models focus on certain aspects of TGF-β1 behaviour and no one model provides a comprehensive story of this regulatory factor''s action. Accordingly our aim was to develop a computational model to act as a complementary approach to improve our understanding of TGF-β1. In our previous study, an agent-based model of keratinocyte colony formation in 2D culture was developed. In this study this model was extensively developed into a three dimensional multiscale model of the human epidermis which is comprised of three interacting and integrated layers: (1) an agent-based model which captures the biological rules governing the cells in the human epidermis at the cellular level and includes the rules for injury induced emergent behaviours, (2) a COmplex PAthway SImulator (COPASI) model which simulates the expression and signalling of TGF-β1 at the sub-cellular level and (3) a mechanical layer embodied by a numerical physical solver responsible for resolving the forces exerted between cells at the multi-cellular level. The integrated model was initially validated by using it to grow a piece of virtual epidermis in 3D and comparing the in virtuo simulations of keratinocyte behaviour and of TGF-β1 signalling with the extensive research literature describing this key regulatory protein. This research reinforces the idea that computational modelling can be an effective additional tool to aid our understanding of complex systems. In the accompanying paper the model is used to explore hypotheses of the functions of TGF-β1 at the cellular and subcellular level on different keratinocyte populations during epidermal wound healing.     

Antimicrobial Peptides from Human Microbiome Against Multidrug Efflux Pump of Pseudomonas aeruginosa: a Computational Study

The excess use of antibiotics has led to the evolution of multidrug-resistant pathogenic strains causing worldwide havoc. These multidrug-resistant strains require potent inhibitors. Pseudomonas aeruginosa is a lead cause of nosocomial infections and also feature in the critical priority list of the world health organization (WHO) for the development of new antibiotics against their antimicrobial resistance. Antimicrobial peptides (AMPs) found in almost every life form from microorganisms to humans are known to defend their hosts against various pathogens. Owing to the diversity of the human microbiome, in this study, we have identified the cell-penetrating AMPs from the human microbiome and studied their inhibitory activity against the outer membrane protein OprM of the MexAB–OprM, a constitutively expressed multidrug efflux pump of the Ps. aeruginosa. Screening of the AMPs from the human microbiome resulted in the identification of 147 cell-penetrating AMPs (CPAMPs). The virtual screening of these CPAMPs against the OprM protein showed significant inhibitory results with the top docked AMP showing binding affinity exceeding ?30 kcal/mol. The molecular dynamic simulation determined the interaction stabilities between the AMPs and the OprM at the binding site. Further, the residue interaction networks (RINs) are analyses to identify the inhibitory patterns. Later, these patterns were confirmed by MM-PBSA analysis suggesting that the AMPs are majorly stabilized by electrostatic interactions at the binding site. Thus, the high binding affinity and insights from the molecular interaction signify that the identified CPAMPs from the human microbiome can be further explored as inhibitory agents against multidrug-resistant Ps. aeruginosa.

     

Computational Prediction of Human Salivary Proteins from Blood Circulation and Application to Diagnostic Biomarker Identification

Proteins can move from blood circulation into salivary glands through active transportation, passive diffusion or ultrafiltration, some of which are then released into saliva and hence can potentially serve as biomarkers for diseases if accurately identified. We present a novel computational method for predicting salivary proteins that come from circulation. The basis for the prediction is a set of physiochemical and sequence features we found to be discerning between human proteins known to be movable from circulation to saliva and proteins deemed to be not in saliva. A classifier was trained based on these features using a support-vector machine to predict protein secretion into saliva. The classifier achieved 88.56% average recall and 90.76% average precision in 10-fold cross-validation on the training data, indicating that the selected features are informative. Considering the possibility that our negative training data may not be highly reliable (i.e., proteins predicted to be not in saliva), we have also trained a ranking method, aiming to rank the known salivary proteins from circulation as the highest among the proteins in the general background, based on the same features. This prediction capability can be used to predict potential biomarker proteins for specific human diseases when coupled with the information of differentially expressed proteins in diseased versus healthy control tissues and a prediction capability for blood-secretory proteins. Using such integrated information, we predicted 31 candidate biomarker proteins in saliva for breast cancer.     

Molecular Cloning of Early-expressed cDNAs from Rice in Response to Infection by Rice Blast Fungus Magnaporthe grisea

Compatible and incompatible reactions in rice plants (Oryza sativa L. cv. Shenxianggen No.4) were resulted from inoculation with two different virulent races of rice blast fungus (Magnaporthe grisea (Hebert) Barr), and thus an effective infecting system was established between rice plants and the rice blast pathogen. Two cDNA clones that showed induced and temporal patterns in expression in the very early stage in response to infection of the fungus were obtained from the plants by use of differential display. Of the two cDNA clones, Fastresp-a was induced to express in both compatible and incompatible interactions although it was expressed earlier in the former reaction. The second one, Fastresp-b, was only expressed in incompatible interaction. Southern blot analysis of the rice genomic DNA indicated that both of the two clones were from genome of the plant. No significant homology to the two genes was found from the rice gene database. This suggested that they were novel genes in rice and may play important roles in rice resistant response to infection of rice blast fungus.     

受稻瘟病原真菌侵染的水稻早期表达基因的cDNA克隆

以亲和性与非亲和性两个稻瘟病原真菌小种（Ｍａｇｎａｐｏｒｔｈｅ ｇｒｉｓｅａ（Ｈｅｂｅｒｔ）Ｂａｒｒ）感染同一水稻品种（Ｏｒｙｚａｓａｔｉｖａ Ｌ．ｃｖ．Ｓｈｅｎｘｉａｎｇｇｅｎｇ Ｎｏ．４）的植株产生明显不同的致病和抗病反应,由此建立了有效的感染系统。应用差异显示技术获得两个在侵染早期具有诱导表达特征的ｃＤＮＡ克隆,其中一个同时在致病和抗病反应中进行早期诱导表达,但在抗病反应中的诱导相对早于其在     

Benthic Reef Primary Production in Response to Large Amplitude Internal Waves at the Similan Islands (Andaman Sea,Thailand)

Coral reefs are facing rapidly changing environments, but implications for reef ecosystem functioning and important services, such as productivity, are difficult to predict. Comparative investigations on coral reefs that are naturally exposed to differing environmental settings can provide essential information in this context. One prevalent phenomenon regularly introducing alterations in water chemistry into coral reefs are internal waves. This study therefore investigates the effect of large amplitude internal waves (LAIW) on primary productivity in coral reefs at the Similan Islands (Andaman Sea, Thailand). The LAIW-exposed west sides of the islands are subjected to sudden drops in water temperature accompanied by enhanced inorganic nutrient concentrations compared to the sheltered east. At the central island, Ko Miang, east and west reefs are only few hundred meters apart, but feature pronounced differences. On the west lower live coral cover (-38 %) coincides with higher turf algae cover (+64 %) and growth (+54 %) compared to the east side. Turf algae and the reef sand-associated microphytobenthos displayed similar chlorophyll a contents on both island sides, but under LAIW exposure, turf algae exhibited higher net photosynthesis (+23 %), whereas the microphytobenthos displayed reduced net and gross photosynthesis (-19 % and -26 %, respectively) accompanied by lower respiration (-42 %). In contrast, the predominant coral Porites lutea showed higher chlorophyll a tissues contents (+42 %) on the LAIW-exposed west in response to lower light availability and higher inorganic nutrient concentrations, but net photosynthesis was comparable for both sides. Turf algae were the major primary producers on the west side, whereas microphytobenthos dominated on the east. The overall primary production rate (comprising all main benthic primary producers) was similar on both island sides, which indicates high primary production variability under different environmental conditions.     

Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought

Reciprocating exchange with other humans requires individuals to infer the intentions of their partners. Despite the importance of this ability in healthy cognition and its impact in disease, the dimensions employed and computations involved in such inferences are not clear. We used a computational theory-of-mind model to classify styles of interaction in 195 pairs of subjects playing a multi-round economic exchange game. This classification produces an estimate of a subject''s depth-of-thought in the game (low, medium, high), a parameter that governs the richness of the models they build of their partner. Subjects in each category showed distinct neural correlates of learning signals associated with different depths-of-thought. The model also detected differences in depth-of-thought between two groups of healthy subjects: one playing patients with psychiatric disease and the other playing healthy controls. The neural response categories identified by this computational characterization of theory-of-mind may yield objective biomarkers useful in the identification and characterization of pathologies that perturb the capacity to model and interact with other humans.     

5种入侵植物补偿反应及其形态可塑性比较

通过模拟刈割试验,研究了5种外来入侵植物(黑麦草、空心莲子草、三叶鬼针草、薇甘菊和胜红蓟)的补偿能力及其形态可塑性。结果表明:多数植物的补偿能力与形态可塑性有一定相关性,刈割和非刈割条件下空心莲子草和薇甘菊都具有较强的形态可塑性,其补偿指数较高,分别为1.65和1.27;多年生黑麦草和三叶鬼针草的形态可塑性在刈割条件下得到增强,补偿指数分别为1.44和1.28;刈割条件下胜红蓟的形态可塑性变化不大或有所降低,其补偿指数最低,为0.82。研究认为,5种植物具有不同的限制其形态可塑性和补偿能力比较理想的刈割时期,薇甘菊攀援生长方式下为30d前和60d后,空心莲子草为60d后,胜红蓟为40～50d,鬼针草为30d前,黑麦草为40～50d。     

Different Levels in Alcohol and Tobacco Consumption in Head and Neck Cancer Patients from 1957 to 2013

Objective

To provide a precise quantification of the association between alcohol and tobacco consumption trends in head and neck cancer patients over the past 45 years.

Methods

We combined findings from all studies published until March 2014 and evaluated the association between different levels in alcohol and tobacco consumption and head and neck cancers through a meta-analytic approach.

Results

We included 28 studies involving 13830 patients with head and neck cancer. In patients with alcohol consumption, the pooled odds ratio (OR) and 95% confidence interval (CI) were 1.29(1.06-1.57), 2.67(2.05-3.48) and 6.63(5.02-8.74) for light drinkers, moderate drinkers and heavy drinkers, respectively. In patients with tobacco consumption, the pooled OR and 95% CI were 2.33(1.84-2.95), 4.97(3.67-6.71) and 6.77(4.81-9.53) for light smokers, moderate smokers and heavy smokers, respectively.

Conclusion

The increased alcohol and tobacco consumption trends increased the risk of head and neck cancer over the past 45 years. Tobacco consumption was found to be a stronger risk factor for head and neck cancer than alcohol consumption. Thus, the control should be considered to limit the intake of alcohol and tobacco.     

末次盛冰期环境恶化对中国北方旧石器文化的影响

末次冰期间冰段时,中国北方地区水热条件普遍较好,旧石器文化也比较发达。然而,进入末次盛冰期后,随着气温的普遍降低和降水量的明显减少,草原和沙漠带急速向南扩张,动物群也大举南迁。对于这种严酷的生存环境,中国北方的旧石器文化是如何响应的呢?本文以宁夏彭阳PY01-02,PY03和PY05等地点的地层剖面和石制品的研究为基础,首先提出彭阳地点群地层沉积相由河湖相沉积迅速转变为黄土堆积说明由末次冰期间冰段到末次盛冰期自然环境发生了剧烈变化。其次,通过对上述两种不同沉积相中出土石制品的大小、重量、原料以及技术上的比较说明随着环境的变化石制品本身也发生了相应的变化。下层河湖相堆积中出土的石制品粗大笨重,主要以各种石英岩为原料,与同期泾水上游旧石器文化的特征相近,应是当地文化特征的一种具体体现。上层马兰黄土中的石制品的普遍较小,主要以石英和燧石为原料,其中用燧石制成的细石器具有宁夏灵武水洞沟下文化层同类制品的特征,而用石英制成的小石器则同海原一带的史前文化有着较为密切的联系,据此作者推测这可能与史前人类在环境日益恶劣的情况下向南迁移有关。山西南部地区的下川和柿子滩遗址的地层和石制品证据亦表明,末次盛冰期前后该地区旧石器文化的明显差异可能也与末次盛冰期环境恶化时人类的迁徙有关。最后,中国北方地区考古遗址的空间分布变化为上述史前人类南迁的推测提供了有力证据。因此,作者认为末次冰期的环境恶化对中国北方旧石器文化的影响具有普遍性。     

三种人全血基因组DNA提取方法的比较

目的：比较改良酚一氯仿抽提法、盐析法、试剂盒法从人全血中提取基因组DNA的效果,以期建立一种快速、经济的提取高质量基因组DNA的方法。方法：分别用上述三种方法从人全血中提取基因组DNA,通过紫外分光光度计、琼脂糖凝胶电泳、聚合酶链式反应（PCR）、限制性内切酶酶切检测提取的基因组DNA的产量、纯度和质量。结果：改良酚一氯仿抽提法与试剂盒法提取的基因组DNA相比,DNA的产量有统计学差异,DNA的纯度无统计学差异,但试剂盒法提取的基因组DNA有较明显的降解现象：盐析法与改良酚．氯仿抽提法、试剂盒法相比,基因组DNA的产量和纯度都存在统计学差异,并且基因组DNA聚合酶链式反应（PCR）扩增的稳定性也明显劣于另外两种方法;三种方法提取基因组DNA均能进行限制性内切核酸消化。结论：改良酚一氯仿抽据取法是一种经济、快速、高效、稳定提取人全血基因组DNA的方法,适用于批量临床标本处理。