Complex Mechanisms of Antimony Genotoxicity in Budding Yeast Involves Replication and Topoisomerase I-Associated DNA Lesions,Telomere Dysfunction and Inhibition of DNA Repair

Antimony is a toxic metalloid with poorly understood mechanisms of toxicity and uncertain carcinogenic properties. By using a combination of genetic, biochemical and DNA damage assays, we investigated the genotoxic potential of trivalent antimony in the model organism Saccharomyces cerevisiae. We found that low doses of Sb(III) generate various forms of DNA damage including replication and topoisomerase I-dependent DNA lesions as well as oxidative stress and replication-independent DNA breaks accompanied by activation of DNA damage checkpoints and formation of recombination repair centers. At higher concentrations of Sb(III), moderately increased oxidative DNA damage is also observed. Consistently, base excision, DNA damage tolerance and homologous recombination repair pathways contribute to Sb(III) tolerance. In addition, we provided evidence suggesting that Sb(III) causes telomere dysfunction. Finally, we showed that Sb(III) negatively effects repair of double-strand DNA breaks and distorts actin and microtubule cytoskeleton. In sum, our results indicate that Sb(III) exhibits a significant genotoxic activity in budding yeast.     

Photocaged Hoechst Enables Subnuclear Visualization and Cell Selective Staining of DNA in vivo

Selective targeting of DNA by means of fluorescent labeling has become a mainstay in the life sciences. While genetic engineering serves as a powerful technique and allows the visualization of nucleic acid by using DNA-targeting fluorescent fusion proteins in a cell-type- and subcellular-specific manner, it relies on the introduction of foreign genes. On the other hand, DNA-binding small fluorescent molecules can be used without genetic engineering, but they are not spatially restricted. Herein, we report a photocaged version of the DNA dye Hoechst33342 (pcHoechst), which can be uncaged by using UV to blue light for the selective staining of chromosomal DNA in subnuclear regions of live cells. Expanding its application to a vertebrate model organism, we demonstrate uncaging in epithelial cells and short-term cell tracking in vivo in zebrafish. We envision pcHoechst as a valuable tool for targeting and interrogating DNA with precise spatiotemporal resolution in living cells and wild-type organisms.     

A New Optimized Wrapper Gene Selection Method for Breast Cancer Prediction

Machine-learning algorithms have been widely used in breast cancer diagnosis to help pathologists and physicians in the decision-making process. However, the high dimensionality of genetic data makes the classification process a challenging task. In this paper, we propose a new optimized wrapper gene selection method that is based on a nature-inspired algorithm (simulated annealing (SA)), which will help select the most informative genes for breast cancer prediction. These optimal genes will then be used to train the classifier to improve its accuracy and efficiency. Three supervised machine-learning algorithms, namely, the support vector machine, the decision tree, and the random forest were used to create the classifier models that will help to predict breast cancer. Two different experiments were conducted using three datasets: Gene expression (GE), deoxyribonucleic acid (DNA) methylation, and a combination of the two. Six measures were used to evaluate the performance of the proposed algorithm, which include the following: Accuracy, precision, recall, specificity, area under the curve (AUC), and execution time. The effectiveness of the proposed classifiers was evaluated through comprehensive experiments. The results demonstrated that our approach outperformed the conventional classifiers as expected in terms of accuracy and execution time. High accuracy values of 99.77%, 99.45%, and 99.45% have been achieved by SA-SVM for GE, DNA methylation, and the combined datasets, respectively. The execution time of the proposed approach was significantly reduced, in comparison to that of the traditional classifiers and the best execution time has been reached by SA-SVM, which was 0.02, 0.03, and 0.02 on GE, DNA methylation, and the combined datasets respectively. In regard to precision and specificity, SA-RF obtained the best result of 100 on GE dataset. While SA-SVM attained the best recall result of 100 on GE dataset.     

Effects of different feeding levels during a 14-week preweaning phase in dairy heifer calves on telomere length and mitochondrial DNA copy number in blood

Telomeres cap the ends of eukaryotic chromosomes, and the telomere length (TL) is related to cellular age. The mitochondrial DNA copy number (mtDNAcn) reflects the abundance of mitochondria in a cell. In addition to generating energy, mitochondria are also the main producers of reactive oxygen species, which in turn can accelerate TL attrition and impair mitochondrial function. Nutrition in early life could influence mtDNAcn and TL in later life. In the present study, we investigated the effects of feeding different levels of milk replacer (MR) on TL shortening and energetic status by examining mtDNAcn of heifers during their first year of life. In this study, whole blood samples were obtained from German Holstein heifer calves 36 to 48 h after birth (wk 1) and at wk 12 and wk 16 of life (n = 37), as well as from 31 calves when reaching 1 yr of age. Calves were fed either a high level of MR (14% solids) at 10 L/d (1.4 kg of MR/d; n = 18) or a restrictive low level at 5.7 L/d (0.8 kg of MR/d; n = 19) until linear weaning in wk 13 to 14 of life. Additional whole blood samples were taken from their respective dams 36 to 48 h after calving. Relative TL (qT) and mtDNAcn in cells from whole blood were measured by multiplex quantitative PCR. The greatest qT values were observed in neonates (36–48 h after birth), with decreasing qT values thereafter. Delta qT values were calculated as ΔqT = qT (first year of life) ? initial qT (36–48 h after birth). We found no effect of the feeding regimen on qT values, but qT decreased with age. The mtDNAcn was lowest in neonates, increased until wk 12 of life, and then remained at a constant level until after weaning (wk 16). After the first year of life, mtDNAcn was decreased and returned to levels comparable to those of the neonatal stage. No differences in mtDNAcn were detectable between feeding groups within each time point. When comparing the values of qT and mtDNAcn between the calves and their dams after calving (36–48 h after birth and after calving), greater values were observed in calves than in dams. Delta qT values were negative in all but 2 calves (on the restricted diet), indicating that the change in TL with age was not uniform among individual animals, whereas no difference in mean ΔqT values occurred between the feeding groups. Additional analyses of the correlation between qT, mtDNAcn, and various indicators of oxidative status from birth until wk 16 of life did not indicate major interactions between oxidative status, qT and mtDNAcn. The results of this study support an age-dependent decrease of TL in calves independent of the MR feeding level and show the dynamic changes of mtDNAcn in early life.     

工业雷管激光编码自动生产线的开发

按工业雷管编码生产工艺要求,采用先进的机电一体化技术设计制造工业雷管激光编码自动生产线。该生产线采用PLC和触摸屏控制操作,计算机配合管理,并备有多点视频监控。经调试及试生产,达到了设计要求。     

浸矿微生物分子生物学鉴定方法

介绍了微生物浸矿中，浸矿微生物的鉴定非常关键，它是对浸矿微生物进行驯化、诱变、基因重组等后续操作的基本前题以及目前分子生物学方法在浸矿微生物鉴定中的应用情况。认为DNA探针分析方法具有快速、灵敏、特异性高等特点，适合混合菌群中已知菌株的快速检出，可应用于未经培养的自然菌群中菌株的鉴定；16SrRNA序列分析方法结果比较准确。     

Changing blood lead levels and DNA damage (comet assay) among immigrant women in Taiwan

Background

International marriage has had a rapid growth in recent years in Taiwan. However, little is known about the blood lead levels and DNA damage levels among immigrant women from resource-limited countries.

Objective

This study (a) explored differences between immigrant women and native women in demographic characteristics, blood lead levels, and DNA damage levels, and (b) identified risk factors that are associated with blood lead concentrations and DNA damage levels after immigration.

Methods

We used a structured questionnaire to collect data on socio-demographic status from (a) 71 immigrant women who had resettled in 2006 in Taichung, Taiwan and (b) 83 native women who live in the same area. Each study participant provided blood samples for lead and metal measurements, complete blood count examination, and the comet assay to measure degree of DNA damage.

Results

Immigrant women had higher mean blood lead concentration (2.23 ± 1.63 vs. 1.63 ± 1.00 μg/dl; p = 0.04) and lower mean blood zinc level (6.22 ± 2.22 vs. 6.89 ± 2.44 mg/l; p = 0.07) than native women. Resettlement time was a determinant to decrease blood lead and DNA damage levels among immigrants in Taiwan. Multiple linear regression analysis confirmed a statistically significant association between blood lead level and DNA damage, while zinc had a protective effect.

Conclusions

Public health agencies should focus on primary prevention and providing screening programs for this vulnerable population. An immigrant women's cohort should been established to follow-up and improve for elevated lead exposure families.     

Exposure and effects assessment of persistent organohalogen contaminants in arctic wildlife and fish

Persistent organic pollutants (POPs) encompass an array of anthropogenic organic and elemental substances and their degradation and metabolic byproducts that have been found in the tissues of exposed animals, especially POPs categorized as organohalogen contaminants (OHCs). OHCs have been of concern in the circumpolar arctic for decades. For example, as a consequence of bioaccumulation and in some cases biomagnification of legacy (e.g., chlorinated PCBs, DDTs and CHLs) and emerging (e.g., brominated flame retardants (BFRs) and in particular polybrominated diphenyl ethers (PBDEs) and perfluorinated compounds (PFCs) including perfluorooctane sulfonate (PFOS) and perfluorooctanic acid (PFOA) found in Arctic biota and humans. Of high concern are the potential biological effects of these contaminants in exposed Arctic wildlife and fish. As concluded in the last review in 2004 for the Arctic Monitoring and Assessment Program (AMAP) on the effects of POPs in Arctic wildlife, prior to 1997, biological effects data were minimal and insufficient at any level of biological organization. The present review summarizes recent studies on biological effects in relation to OHC exposure, and attempts to assess known tissue/body compartment concentration data in the context of possible threshold levels of effects to evaluate the risks. This review concentrates mainly on post-2002, new OHC effects data in Arctic wildlife and fish, and is largely based on recently available effects data for populations of several top trophic level species, including seabirds (e.g., glaucous gull (Larus hyperboreus)), polar bears (Ursus maritimus), polar (Arctic) fox (Vulpes lagopus), and Arctic charr (Salvelinus alpinus), as well as semi-captive studies on sled dogs (Canis familiaris). Regardless, there remains a dearth of data on true contaminant exposure, cause-effect relationships with respect to these contaminant exposures in Arctic wildlife and fish. Indications of exposure effects are largely based on correlations between biomarker endpoints (e.g., biochemical processes related to the immune and endocrine system, pathological changes in tissues and reproduction and development) and tissue residue levels of OHCs (e.g., PCBs, DDTs, CHLs, PBDEs and in a few cases perfluorinated carboxylic acids (PFCAs) and perfluorinated sulfonates (PFSAs)). Some exceptions include semi-field studies on comparative contaminant effects of control and exposed cohorts of captive Greenland sled dogs, and performance studies mimicking environmentally relevant PCB concentrations in Arctic charr. Recent tissue concentrations in several arctic marine mammal species and populations exceed a general threshold level of concern of 1 part-per-million (ppm), but a clear evidence of a POP/OHC-related stress in these populations remains to be confirmed. There remains minimal evidence that OHCs are having widespread effects on the health of Arctic organisms, with the possible exception of East Greenland and Svalbard polar bears and Svalbard glaucous gulls. However, the true (if any real) effects of POPs in Arctic wildlife have to be put into the context of other environmental, ecological and physiological stressors (both anthropogenic and natural) that render an overall complex picture. For instance, seasonal changes in food intake and corresponding cycles of fattening and emaciation seen in Arctic animals can modify contaminant tissue distribution and toxicokinetics (contaminant deposition, metabolism and depuration). Also, other factors, including impact of climate change (seasonal ice and temperature changes, and connection to food web changes, nutrition, etc. in exposed biota), disease, species invasion and the connection to disease resistance will impact toxicant exposure. Overall, further research and better understanding of POP/OHC impact on animal performance in Arctic biota are recommended. Regardless, it could be argued that Arctic wildlife and fish at the highest potential risk of POP/OHC exposure and mediated effects are East Greenland, Svalbard and (West and South) Hudson Bay polar bears, Alaskan and Northern Norway killer whales, several species of gulls and other seabirds from the Svalbard area, Northern Norway, East Greenland, the Kara Sea and/or the Canadian central high Arctic, East Greenland ringed seal and a few populations of Arctic charr and Greenland shark.     

非编码DNA的研究

根据生物体长期进化所产生的“fail-safe”效应,着重讨论了占基因组98％以上的非编码DNA序列的生物学功能;分析了密码子-氨基酸矩阵、密码子-反密码子矩阵在DNA复制、转录过程中防止基因突变的摇摆(Wobble)现象;阐明了基因结构中非编码“内含子”提高转录过程的可靠性;揭示了基因组中全部非编码DNA,特别是重复序列中的“转座子”在基因组中散在插入特性,构成了基因组的骨架——基因载体,对DNA分子的结构稳定性起了关键作用,从而可以减轻,乃至“屏蔽”恶劣的细胞环境对基因的干扰和损伤．     

二维码位流长度最小化算法

目的 快速响应矩阵码(quick response code,QR code)简称二维码,是一种由深色和浅色模块组成的正方形符号。给定输入数据,不同编码算法可能输出不同的位流。位流长度决定了二维码的版本,进而决定了二维码每条边上的模块数量。减小二维码的版本能够在不减小模块大小的前提下节省面积,或者在不改变面积的前提下增大模块大小。为了减小二维码面积、提高二维码识读率,本文提出了位流长度最小化算法。方法 首先,根据二维码位流可以分段切换编码模式的特点,归纳了6种编码状态;然后,根据二维码位流编码标准推导了状态转移关系,从而将位流长度最小化问题转换成动态规划问题;最后,通过求解动态规划问题,计算出最短位流。针对统一资源定位符(uniform resource locator,URL)类型数据,利用其部分字段对大小写不敏感、部分字段可以转义的性质,提出了统一资源定位符的最短位流计算算法,进一步缩短位流。结果 本文构建了一个测试集,包含603个编码了非URL数据的二维码,以及1 679个编码了URL数据的二维码。实验结果表明,本文算法与二维码标准相比,对于非URL测试集,位流长度减小的二维码占比9.1%,版本减小的二维码占比1.2%;对于URL测试集,位流长度减小的二维码占比98.4%,版本减小的二维码占比31.7%。结论 二维码位流长度最小化算法输出的位流长度最短,输出的二维码版本最小,能在兼容标准二维码解码器且不影响纠错能力的前提下提升二维码的数据容量。同时,本文算法运行速度快,易于使用,没有需要调节的参数。