Specific PCR product primer design using memetic algorithm

To provide feasible primer sets for performing a polymerase chain reaction (PCR) experiment, many primer design methods have been proposed. However, the majority of these methods require a relatively long time to obtain an optimal solution since large quantities of template DNA need to be analyzed. Furthermore, the designed primer sets usually do not provide a specific PCR product size. In recent years, evolutionary computation has been applied to PCR primer design and yielded promising results. In this article, a memetic algorithm (MA) is proposed to solve primer design problems associated with providing a specific product size for PCR experiments. The MA is compared with a genetic algorithm (GA) using an accuracy formula to estimate the quality of the primer design and test the running time. Overall, 50 accession nucleotide sequences were sampled for the comparison of the accuracy of the GA and MA for primer design. Five hundred runs of the GA and MA primer design were performed with PCR product lengths of 150–300 bps and 500–800 bps, and two different methods of calculating T_m for each accession nucleotide sequence were tested. A comparison of the accuracy results for the GA and MA primer design showed that the MA primer design yielded better results than the GA primer design. The results further indicate that the proposed method finds optimal or near‐optimal primer sets and effective PCR products in a dry dock experiment. Related materials are available online at http://bio.kuas.edu.tw/ma‐pd/ . © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry

Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three‐dimensional structure determination of the ordered regions of proteins by NMR methods. In this article, we demonstrate the application of ¹H/²H exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N‐ and C‐terminal tails were evaluated using ¹H‐¹⁵N HSQC and ¹H‐¹⁵N heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMS‐based truncated construct for a 77‐residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Mud-puddling in the yellow-spined bamboo locust, Ceracris kiangsu (Oedipodidae: Orthoptera): Does it detect and prefer salts or nitrogenous compounds from human urine?

C. kiangsu adults were observed visiting human urine, especially on hot summer days. The main chemicals in fresh human urine include inorganic salts and CO(NH₂)_2. When human urine was incubated, NH₄HCO₃ became the richest nitrogenous compound. The phagostimulants, repellents and attractants in urine were identified here. On the filter papers treated with fresh or incubated urine samples, the 5th instar nymphs and the adults started and continued gnawing around the edges, in contrast to the 3rd and the 4th instar nymphs. The consumed areas were dramatically greater on the filters treated with the urine samples incubated for 3-6 days. The feedings of both male and female adults were also stimulated by several urine-borne components such as NaCl, NaH₂PO₄, Na₂SO₄, KCl, NH₄Cl and NH₄HCO₃ but not by CO(NH₂)₂. Among them NaCl was the most powerful phagostimulant. The repelling, or attractive/arresting effects of CO(NH₂)₂ and NH₄HCO₃ were also evaluated by a two-choice test. When exposed to water- and CO(NH₂)₂ solution-immersed filters simultaneously, the adults prefer to stay on water-immersed filter. In contrast, when provided water- and NH₄HCO₃ solution-treated filters, the adults prefer to stay on NH₄HCO₃ solution-treated filter. This demonstrated that CO(NH₂)₂ acted as a repellent and NH₄HCO₃ as an attractant/arrestant. In the bamboo forest, similar feeding behavior was also elicited by NaCl, NH₄HCO₃ but not by CO(NH₂)₂. Comparing to NaCl solution, a mixed solution of NaCl and CO(NH₂)₂ (1:1) significantly decreased the consumed area of the treated filters whereas a mixed solution of NaCl and NH₄HCO₃ (1:1) dramatically increased the consumed area. These results demonstrated that the phagostimulatory effect by NaCl was reduced by CO(NH₂)₂ in fresh urine and was enhanced by NH₄HCO₃ in incubated urine.     

Glucose biosensor based on electrodeposited platinum nanoparticles and three-dimensional porous chitosan membranes

The chitosan with three-dimensional porous structure greatly increased the effective electrode surface for loading of platinum nanoparticles and promoted efficient electron transfer. The resulting biosensor had a response time (within 5 s) and a linear response from 6 μM to 4.2 mM glucose with a detection limit of 2 μM (S/N = 3). Moreover, the methodology can be applied for the immobilization of other enzymes.     

The configuration,solvatochromism and metallo‐responses of two novel cyano‐containing oligo(phenylene‐vinylene) derivatives

Two novel cyano‐containing oligo(phenylenevinylene) (OPV) derivatives have been designed and synthesized. Photophysical and sensing properties of the two compounds were studied. Such studies reveal the intramolecular charge transfer process between cyano groups and OPV core. The results showed that the alkyl difference of substituted OPV leads to the changes of molecular configuration and metallo‐response of two compounds. Copyright © 2010 John Wiley & Sons, Ltd.     

Hyper-activated pro-inflammatory CD16 monocytes correlate with the severity of liver injury and fibrosis in patients with chronic hepatitis B

Background

Extensive mononuclear cell infiltration is strongly correlated with liver damage in patients with chronic hepatitis B virus (CHB) infection. Macrophages and infiltrating monocytes also participate in the development of liver damage and fibrosis in animal models. However, little is known regarding the immunopathogenic role of peripheral blood monocytes and intrahepatic macrophages.

Methodology/Principal Findings

The frequencies, phenotypes, and functions of peripheral blood and intrahepatic monocyte/macrophage subsets were analyzed in 110 HBeAg positive CHB patients, including 32 immune tolerant (IT) carriers and 78 immune activated (IA) patients. Liver biopsies from 20 IA patients undergoing diagnosis were collected for immunohistochemical analysis. IA patients displayed significant increases in peripheral blood monocytes and intrahepatic macrophages as well as CD16⁺ subsets, which were closely associated with serum alanine aminotransferase (ALT) levels and the liver histological activity index (HAI) scores. In addition, the increased CD16⁺ monocytes/macrophages expressed higher levels of the activation marker HLA-DR compared with CD16⁻ monocytes/macrophages. Furthermore, peripheral blood CD16⁺ monocytes preferentially released inflammatory cytokines and hold higher potency in inducing the expansion of Th17 cells. Of note, hepatic neutrophils also positively correlated with HAI scores.

Conclusions

These distinct properties of monocyte/macrophage subpopulations participate in fostering the inflammatory microenvironment and liver damage in CHB patients and further represent a collaborative scenario among different cell types contributing to the pathogenesis of HBV-induced liver disease.     

A model on liquid penetration into soft material with application to needle-free jet injection

A mathematical model has been presented for a high speed liquid jet penetration into soft solid by a needle-free injection system. The model consists of a cylindrical column formed by the initial jet penetration and an expansion sphere due to continuous deposition of the liquid. By solving the equations of energy conservation and volume conservation, the penetration depth and the radius of the expansion sphere can be predicted. As an example, the calculation results were presented for a typical needle-free injection system into which a silicon rubber was injected into. The calculation results were compared with the experimental results.     

Proteomic Analysis of Interactions Between the Generalist Herbivore <Emphasis Type="Italic">Spodoptera exigua</Emphasis> (Lepidoptera: Noctuidae) and <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

In this study, comparative proteomics was used to investigate the interaction of Spodoptera exigua and Arabidopsis thaliana. By using 2-D electrophoresis of differentially expressed proteins, combined with high-throughput matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and MALDI-TOF/TOF MS, the changes in the abundance of proteins induced by insect feeding were studied in A. thaliana. More than 1,100 protein spots were reproducibly detected on each gel. The intensities of 30 protein spots in particular changed significantly, showing differences in volume of at least twofold. Among these, 17 protein spots were upregulated, and 13 were downregulated following an 8-h insect feeding period. Nineteen insect-feeding-responsive proteins were identified, all of which were involved in metabolic regulation, binding functions or cofactor requirement of protein, cell rescue, and defense and virulence, as assessed by Munich Information Center for Protein Sequences function category. About 50% of these were involved in metabolism, including transketolase, S-adenosylmethionine synthase 3, 2,3-biphosphoglycerate-independent phosphoglycerate mutase, beta-ureidopropionase, GDP-d-mannose 3′,5′-epimerase, and fatty acid synthase. The identification of insect-feeding-responsive proteins on Arabidopsis provides not only new insights into insect stress but also a good start for further investigation of their functions. Understanding how the plant responses to insects in the proteomic level will provide tools for a better management of insect pest in the field.     

奶牛乳腺脂肪酸合成相关基因研究进展

数量和种类繁多的脂肪酸构成了牛奶中不同分子量和饱和度的甘油三酯,也是乳脂的主要成分.链长不同的脂肪酸来源也不尽相同,几乎所有的短链和中链脂肪酸都由乳腺内源合成,长链脂肪酸主要是由血液中转运而来,奶牛乳腺在转运和合成脂肪酸过程中起着重要作用.近年来,研究人员将传统营养与分子生物学研究相结合,发现了大量与乳脂合成相关基因,并揭示了其功能和相互之间的作用.就奶牛乳腺的脂肪酸摄取和转运,脂肪酸的内源合成,乳腺重要酶类,脂肪酸酯化和相关基因网络调控几方面对脂肪酸合成相关基因进行归类,对其研究进展进行介绍.