Calculation of line tension in various models of lipid bilayer pore edge

The line tension of the edge of the lipid bilayer pore is calculated on the basis of the elastic theory of continuous liquid-crystal medium. Three types of deformations of the membrane were taken into account: bending, lateral stretching/compression, and tilt of the lipidic tails. Various models of structure of the pore edge are considered: models of the cylindrical shape with given radius and optimum radius, “extrapolational” model, “two-coordinate” model, and model with a hydrophobic cavity (“void”). Models can be conventionally divided into two classes. The first class includes models in which membrane monolayers are in contact with each other everywhere. Models of the second class admit appearance of a hydrophobic cavity between monolayers. Models of the first class yield value of the line tension γ, strongly differing from that known from the literature (～10 pN). For example, the value of the line tension γ obtained in the cylindrical model equals to 21 pN; in the two-coordinate model, 19 pN, and in the extrapolational model, 62 pN. At the same time, the model with cavity gives the value of γ eqal ～10 pN, provided that surface tension at the boundary of the lipid tails is close to zero. This value is in a good agreement with the literature data.     

On‐line adaptive metabolic flux analysis: Application to PHB production by mixed microbial cultures

In this work, an algorithm for on‐line adaptive metabolic flux analysis (MFA) is proposed and applied to polyhydroxybutyrate (PHB) production by mixed microbial cultures (MMC). In this process, population dynamics constitutes an important source of perturbation to MFA calculations because some stoichiometric and energetic parameters of the underlying metabolic network are continuously changing over time. The proposed algorithm is based on the application of the observer‐based estimator (OBE) to the central MFA equation, whereby the role of the OBE is to force the accumulation of intracellular metabolites to converge to zero by adjusting the values of unknown network parameters. The algorithm was implemented in a reactor equipped with on‐line analyses of dissolved oxygen and carbon dioxide through respirometric and titrimetric measurements. The oxygen and carbon dioxide fluxes were measured directly, whereas acetate, PHB, and sludge production fluxes were estimated indirectly using a projection of latent structures model calibrated a priori with off‐line measurements. The algorithm was implemented in a way that the network parameters associated with biosynthesis were adjusted on‐line. The algorithm proofed to converge exponentially with the steady state error always below 1 mmol/L. The estimated fluxes passed the consistency index test for experimental error variances as low as 1%. The comparison of measured and estimated respiratory coefficient and of the theoretical and estimated yield of sludge on acetate further confirmed the metabolic consistency of the parameters that were estimated on‐line. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Data reconciliation of concentration estimates from mid‐infrared and dielectric spectral measurements for improved on‐line monitoring of bioprocesses

Real‐time data reconciliation of concentration estimates of process analytes and biomass in microbial fermentations is investigated. A Fourier‐transform mid‐infrared spectrometer predicting the concentrations of process metabolites is used in parallel with a dielectric spectrometer predicting the biomass concentration during a batch fermentation of the yeast Saccharomyces cerevisiae. Calibration models developed off‐line for both spectrometers suffer from poor predictive capability due to instrumental and process drifts unseen during calibration. To address this problem, the predicted metabolite and biomass concentrations, along with off‐gas analysis and base addition measurements, are reconciled in real‐time based on the closure of mass and elemental balances. A statistical test is used to confirm the integrity of the balances, and a non‐negativity constraint is used to guide the data reconciliation algorithm toward positive concentrations. It is verified experimentally that the proposed approach reduces the standard error of prediction without the need for additional off‐line analysis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

草木犀石油醚提取物对小鼠巨噬细胞促炎介质的影响

目的研究草木犀石油醚提取物在体外的抗炎作用。方法采用小鼠巨噬细胞系RAW264．7建立炎症细胞模型,加入10μg/L的LPS培养液和不同浓度的草木犀石油醚提取物进行干预。ELISA法检测上清液中TNF-α,IL-1β,IL-6和NO的分泌量;实时荧光定量RT-PCR检测TNF-α,iNOS和COX-2的mRNA表达;Western印迹法检测COX-2蛋白的表达。结果草木犀提取物干预后细胞所分泌的炎性介质（TNF—α,IL-1β,IL-6和NO）与模型组相比均显著降低（P〈0．01）,并存在剂量依赖关系;RT-PCR结果显示干预后细胞TNF-α,iNOS和COX-2的mRNA表达水平显著降低（P〈0．01）,也存在剂量依赖关系;Western印迹结果显示草木犀石油醚提取物及地塞米松干预后COX-2蛋白水平明显降低（P〈0．01）。结论草木犀的石油醚提取物通过下调LPS诱导的巨噬细胞表达炎性介质而发挥其体外抗炎作用,且其下调作用呈剂量依赖性。     

5个籼稻背景的高代回交置换系的置换片段分析

以轮回亲本籼稻品种9311（Oryza sativassp.indica‘Yangdao6’）为对照,选用132个亲本间有多态性的SSR标记,对以粳稻品种日本晴（Oryzasativassp.japonica‘Nipponbare’）为供体的5个高代回交置换系的农艺性状及置换片段进行分析。5个置换系在粒长、粒宽、千粒重、剑叶长、株高及落粒性等方面与籼稻品种9311之间有极显著差异,其余性状与籼稻品种9311间的差异不显著;从置换系中检测出8个置换片段,总长度为236.0cM,平均长度为29.5cM;从置换片段上检出包括2个千粒重、1个粒长、1个粒宽、1个剑叶长、1个株高和1个落粒性共7个QTLs,分别分布在水稻第1、3、5、6和第10染色体上。其中,第1染色体上控制剑叶长的QTL和第6染色体上控制株高的QTL可能是新发现的QTLs。实验结果进一步丰富了置换系群体的数量和质量,也为QTLs的精细定位及分子设计育种奠定了基础。     

改进重叠延伸法引入DNA定点突变的新方法

目的：改进重叠延伸PCR法,实现一种引入DNA定点突变的准确简便方法。方法：通过应用不同的扩增酶和反应体系,以重叠延伸PCR的方法产生引入突变位点的DNA片断,然后再亚克隆到载体中。该文以人cyclin D1启动子的NF-κB位点（-39/-30）为例。结果：通过DNA测序证明定点突变成功引入。一次引入4个突变碱基。突变引入率为100%。     

Distinguishing range expansions from previously undocumented populations using background data from museum records

Aim Knowledge of the distribution of a species is fundamental to understanding the species’ biology, and changes in known distribution may reflect response to environmental change. However, in many cases, purported range expansions are not adequately justified and extra‐limital records may simply reflect previously undocumented populations. Thus, it is critical to distinguish between these hypotheses. This study aimed to provide a simple, conceptual framework for evaluating these hypotheses that depends on the use of museum background data to assess the adequacy of historical sampling. Location American Southwest and worldwide. Methods Background data are records of species other than the taxon of interest that are likely to be documented using the same sampling methods. If evaluation of the background group determines that the taxon of interest would have been documented if present, then the extra‐limital record can be considered a range expansion. Conversely, if evaluation of the background group indicates that historical sampling was inadequate to have documented the taxon of interest, then the most parsimonious explanation for the extra‐limital record is an undocumented population, which should be presented as a range extension. As an example, I applied the methods to a purported range expansion of the yellow‐nosed cotton rat (Sigmodon ochrognathus) in the Rincon Mountains in south‐eastern Arizona. Results Evaluation of the background group revealed that sampling was inadequate to have documented S. ochrognathus in the Rincon Mountains if present. Thus, the record of S. ochrognathus in the Rincon Mountains was interpreted as a previously undocumented population rather than a range expansion. Main conclusion Range expansions can reflect factors that are of important conservation concern, such as climate change or habitat modification. Thus, it is essential that the cause of extra‐limital records be accurately interpreted. The method provides a simple means for testing between hypotheses of range extension and range expansion.     

Sustained viral activity of epstein-Barr virus contributes to cellular immortalization of lymphoblastoid cell lines

EBV-transformed lymphoblastoid cell lines (LCLs) are used as a resource for human genetic, immunological, and pharmacogenomic studies. We investigated the biological activity of 20 LCL strains during continuous long-term subculture up to a passage number of 160. Out of 20 LCL strains, 17 proliferated up to a passage number of 160, at which point LCLs are generally considered as “immortalized”. The other three LCL strains lost the ability to proliferate at an average passage number of 41, during which these LCLs may have undergone cellular crisis. These non-immortal LCL strains exhibited no telomerase activity, decreased EBV gene expression, and a lower copy number of the EBV genome and mitochondrial DNA when compared with immortal LCLs. Thus, this study suggests that sustained EBV viral activity as well as telomerase activity may be required for complete LCL immortalization. These authors contributed equally to this work.     

Predicting response to platinum and non-platinum drugs through bioluminescence resonance energy transfer (BRET) based bio-molecular interactions in platinum resistant epithelial ovarian cancer

Therapy induced rewiring of signalling networks often lead to acquirement of platinum-resistance, thereby necessitating the use of non-platinum agents as second-line treatment particularly for epithelial ovarian cancer (EOC). A prior subject-specific assessment can guide the choice of optimal non-platinum agent/s and possible targeted therapeutic/s. Assessment of protein-protein interactions are superior to simple cytotoxicity assays to determine therapeutic efficacy and associated molecular responses. Utilizing improved PIP3-AKT and ERK1/2 activation Bioluminescence Resonance Energy Transfer (BRET) sensors, we report chemotherapy-induced ERK1/2 activation predominantly in cisplatin-paclitaxel resistant EOC cells and increased activation of both ERK1/2 and AKT in malignant ascites derived cancer cells from platinum-resistant patients but not from treatment-naive or platinum-sensitive relapse patients. Further, majority of the non-platinum drugs except irinotecan increased ERK1/2 activation in platinum-taxol resistant cells as observed by live-cell BRET assessment which were associated with p90RSK1/2 and BAD activation along with upregulation of multidrug transporter gene ABCC1 and cell survival genes like cyclin D1 and Bcl2. Interestingly, only irinotecan was able to sensitize these resistant cells. Altogether, this first report of BRET based sensing of molecular pathway activations in platinum resistant cell lines and patient's derived cancer cells highlight the clinical potential of BRET sensors in management of therapy resistant cancer.     

Comparison of genetic and cytogenetic maps of hexaploid wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) using SSR and DArT markers

A number of technologies are available to increase the abundance of DNA markers and contribute to developing high resolution genetic maps suitable for genetic analysis. The aim of this study was to expand the number of Diversity Array Technology (DArT) markers on the wheat array that can be mapped in the wheat genome, and to determine their chromosomal location with respect to simple sequence repeat (SSR) markers and their position on the cytogenetic map. A total of 749 and 512 individual DArT and SSR markers, respectively, were identified on at least one of four genetic maps derived from recombinant inbred line (RIL) or doubled haploid (DH) populations. A number of clustered DArT markers were observed in each genetic map, in which 20–34% of markers were redundant. Segregation distortion of DArT and SSR markers was also observed in each mapping population. Only 14% of markers on the Version 2.0 wheat array were assigned to chromosomal bins by deletion mapping using aneuploid lines. In this regard, methylation effects need to be considered when applying DArT marker in genetic mapping. However, deletion mapping of DArT markers provides a reference to align genetic and cytogenetic maps and estimate the coverage of DNA markers across the wheat genome. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.