http://www.hindawi.comThe latest articles from Hindawi Publishing Corporation© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/728908Daniel Howard© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/564969Vascular endothelial cell growth inhibitor (VEGI) is a recently identified antiangiogenic cytokine that belongs to the TNF superfamily, and could effectively inhibit endothelial cell proliferation and angiogenesis. Synthetic peptide CTT (CTTHWGFTLC) has been found to suppress invasion and migration of both tumor and endothelial cells by potent and selective inhibition of MMP-2 and MMP-9. To prepare chimeric protein VEGI-CTT for more potent antitumor therapy, the recombinant expression vector pET-VEGI-CTT was constructed. This fusion protein was expressed in inclusion bodies in E. coli BL21 (DE3), and was refolded and purified by immobilized metal affinity chromatography using His-tag. Purified VEGI-CTT protein was characterized by proliferation assays of the endothelial cells and casein degradation assay in vitro. The results demonstrated that chimeric protein VEGI-CTT had a potent activity of antiangiogenesis through inhibiting the proliferation of endothelial cells, and could effectively reduce the activity of MMP-2 and MMP-9. The preliminarily in vivo study demonstrated that chimeric protein VEGI-CTT had more potent antitumor activity than VEGI and/or CTT peptide against CA46 human lymphoma xenografts in nude mice. Thus, these facts that are derived from the present study suggest that the chimeric protein VEGI-CTT may be used for tumor therapy in the future.Jiping Cai, Ruili Wei, and Jinwei Cheng© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/692573The gene encoding the cyclodextrin glycosyltransferase (CGTase) of Paenibacillus pabuli US132, previously described as efficient antistaling agent and good candidate for cyclodextrins production, was cloned, sequenced, and expressed in Escherichia coli. Sequence analysis showed that the mature enzyme (684 amino acids) was preceded by a signal peptide of 34 residues. The enzyme exhibited the highest identity (94%) to the β-CGTase of Bacillus circulans no. 8. The production of the recombinant CGTase, as active form, was very low (about 1 U/mL) in shake flasks at 37∘C. This production reached 22 U/mL after 22 hours of induction by mainly shifting the postinduction temperature from 37 to 19∘C and using 2TY instead of LB medium. High enzyme production (35 U/mL) was attained after 18 hours of induction in fermentor using the same culture conditions as in shake flask. The recombinant enzyme showed Vmax⁡ and Km values of 253±36 μmol of β-cyclodextrin/mg/min and 0.36±0.18 g/L, respectively.Sonia Jemli, Ezzedine Ben Messaoud, Sameh Ben Mabrouk, and Samir Bejar© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/346129This paper describes the application of the alternating Kernel mixture (AKM) segmentation algorithm to high resolution MRI subvolumes acquired from a 1.5T scanner (hippocampus, n=10 and prefrontal cortex, n=9) and a 3T scanner (hippocampus, n=10 and occipital lobe, n=10). Segmentation of the subvolumes into cerebrospinal fluid, gray matter, and white matter tissue is validated by comparison with manual segmentation. When compared with other segmentation methods that use traditional Bayesian segmentation, AKM yields smaller errors (P<.005, exact Wilcoxon signed rank test) demonstrating the robustness and wide applicability of AKM across different structures. By generating multiple mixtures for each tissue compartment, AKM mimics the increased variation of manual segmentation in partial volumes due to the highly folded tissues. AKM's superior performance makes it useful for tissue segmentation of subcortical and cortical structures in large-scale neuroimaging studies.Nayoung A. Lee, Carey E. Priebe, Michael I. Miller, and J. Tilak Ratnanather© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/495436Hepatitis B virus (HBV) constitutes a serious menace to man. DNA recombination and sequencing, interspecific in vitro fertilization, single-embryo PCR and RT-PCR were employed to establish a sensitive and rapid assay for exploring the vertical transmission of viruses via male germ line. Plasmid pIRES2-EGFP-HBs which expressed enhanced green fluorescent protein as reporter for the expression of hepatitis B virus S gene was successfully constructed and confirmed by PCR, EcoR I and Sal I digestion, and DNA sequencing. After exposure to the plasmid, human spermatozoa were used to fertilize with zona-free hamster ova. Two-cell embryos were collected and classified into group A with green fluorescence and group B without green fluorescence under fluorescence microscope. The results showed that HBs DNA positive bands were detected in the embryos with green fluorescence (PCR and RT-PCR) and positive control (PCR) indicating expression of pIRES2-EGFP-HBs, and not observed in the embryos without green fluorescence and negative controls (PCR and RT-PCR) indicating no pIRES2-EGFP-HBs in the cells. The advantages and application foreground of this assay for study on vertical transmission of viruses such as HCV, HIV, HPV, and SARS via germ line were discussed.Mohamed Morsi M. Ahmed, Tian-Hua Huang, and Qing-Dong Xie© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/526343In nationwide mammography screening, thousands of mammography examinations must be processed. Each consists of two standard views of each breast, and each mammogram must be visually examined by an experienced radiologist to assess it for any anomalies. The ability to detect an anomaly in mammographic texture is important to successful outcomes in mammography screening and, in this study, a large number of mammograms were digitized with a highly accurate scanner; and textural features were derived from the mammograms as input data to a SONNET selforganizing neural network. The paper discusses how SONNET was used to produce a taxonomic organization of the mammography archive in an unsupervised manner. This process is subject to certain choices of SONNET parameters, in these numerical experiments using the craniocaudal view, and typically produced O(10), for example, 39 mammogram classes, by analysis of features from O(103) mammogram images. The mammogram taxonomy captured typical subtleties to discriminate mammograms, and it is submitted that this may be exploited to aid the detection of mammographic anomalies, for example, by acting as a preprocessing stage to simplify the task for a computational detection scheme, or by ordering mammography examinations by mammogram taxonomic class prior to screening in order to encourage more successful visual examination during screening. The resulting taxonomy may help train screening radiologists and conceivably help to settle legal cases concerning a mammography screening examination because the taxonomy can reveal the frequency of mammographic patterns in a population.Daniel Howard, Simon C. Roberts, Conor Ryan, and Adrian Brezulianu© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/632424Toxoplasma gondii is an obligate intracellular protozoan parasite classified in the phylum Apicomplexa, which includes numerous notable human and animal pathogens (Plasmodium species, Cryptosporidium species, Neospora caninum, etc.). The invasive stages of apicomplexans are characterized by the presence of an apical complex composed of specialized cytoskeletal and secretory organelles, including rhoptries. Rhoptries, unique apical secretory organelles shared exclusively by all apicomplexan parasites, are known to be involved in an active parasite's penetration into the host cell associated with the biogenesis of specific intracellular compartment, parasitophorous vacuole in which the parasite multiplies intensively, avoiding intracellular killing. Due to the key biological role of rhoptries, rhoptry proteins have recently become vaccine candidates for the prevention of several parasitoses, toxoplasmosis among them. The article presents current data on T. gondii rhoptries biology and new approaches to the development of effective vaccines against toxoplasmosis using rhoptry antigens.Henryka Dlugonska© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/394802We examined the antiproliferation effect of Jaceosidin (4′, 5, 7-trihydroxy-3′, 6-dimethoxyflavone) isolated from the herb of Artemisia vestita Wall on several human cancer cell lines. Jaceosidin significantly reduced the proliferation of CAOV-3, SKOV-3, HeLa, and PC3 cells in a concentration-dependent manner. A time-dependent inhibition was also observed in CAOV-3 cells by Jaceosidin. By flow cytometric analysis, we found that Jaceosidin treatment resulted in an increased apoptosis in CAOV-3 cells. The cells treated with Jaceosidin exhibited a decreased mitochondrial membrane potential. Jaceosidin also increased the level of cleaved caspase-9 and induced the cleavage of caspase-3 and poly (ADP-ribose) polymerase (PARP), while caspase-3 inhibitor Z-DEVD-FMK significantly reversed the proapoptotic effect of Jaceosidin in CAOV-3 cells. Moreover, Jaceosidin elevated the level of cytochrome c in cytosol. These findings suggest that the anticancer effect of Jaceosidin may be contributed by an induction of apoptosis involving cytochrome c release from mitochondria to cytosol.Wen Lv, Xia Sheng, Ting Chen, Qiang Xu, and Xing Xie© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/736060Human thymosin alpha 1 (Tα1) is an important peptide in the development and senescence of immunological competence in human, and many studies have reported the expression of this peptide. In this study, we designed and synthesized the Tα1 gene according to the E. coli codon usage preference and constructed a 6×Tα1 concatemer. The latter was inserted into an E. coli expression vector pET-22b (+), and transformed into E. coli BL21 (DE3). After induction with IPTG, the concatemer protein was successfully expressed in E. coli then cleaved by hydroxylamine to release the Tα1 monomer. Gly-SDS-PAGE and mass spectrometry confirmed that the recombinant protein was cleaved as intended. The bioactivity of the Tα1 monomer was analyzed by lymphocyte proliferation and by mitochondrial activity in two different tumor cell lines. This study provides a description of the preparation of a bioactive Tα1, which may prove useful in future biomedical research.Liang Zhou, Zong-Teng Lai, Min-Kan Lu, Xing-Guo Gong, and Yi Xie© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/597913The traditional experimental approaches used for changing the flux or the concentration of a particular metabolite of a metabolic pathway have been mostly based on the inhibition or over-expression of the presumed rate-limiting step. However, the attempts to manipulate a metabolic pathway by following such approach have proved to be unsuccessful. Metabolic Control Analysis (MCA) establishes how to determine, quantitatively, the degree of control that a given enzyme exerts on flux and on the concentration of metabolites, thus substituting the intuitive, qualitative concept of rate limiting step. Moreover, MCA helps to understand (i) the underlying mechanisms by which a given enzyme exerts high or low control and (ii) why the control of the pathway is shared by several pathway enzymes and transporters. By applying MCA it is possible to identify the steps that should be modified to achieve a successful alteration of flux or metabolite concentration in pathways of biotechnological (e.g., large scale metabolite production) or clinical relevance (e.g., drug therapy). The different MCA experimental approaches developed for the determination of the flux-control distribution in several pathways are described. Full understanding of the pathway properties when is working under a variety of conditions can help to attain a successful manipulation of flux and metabolite concentration.Rafael Moreno-Sánchez, Emma Saavedra, Sara Rodríguez-Enríquez, and Viridiana Olín-Sandoval© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/163902Obesity has been linked with an increased risk of prostate cancer. The formation of toxic free oxygen radicals has been implicated in obesity mediated disease processes. Leptin is one of the major cytokines produced by adipocytes and controls body weight homeostasis through food intake and energy expenditure. The rationale of the study was to determine the impact of leptin on the metastatic potential of androgen-sensitive (LNCaP) cells as well as androgen-insensitive (PC-3 and DU-145) cells. At a concentration of 200_nm, LNCaP cells showed a significant increase (20% above control; P<.0001) in cellular proliferation without any effect on androgen-insensitive cells. Furthermore, exposure to leptin caused a significant (P<.01 to P<.0001) dose-dependent decrease in migration and invasion of PC3 and Du-145 prostate carcinoma cell lines. At the molecular level, exposure of androgen-independent prostate cancer cells to leptin stimulates the phosphorylation of MAPK at early time point as well as the transcription factor STAT3, suggesting the activation of the intracellular signaling cascade upon leptin binding to its cognate receptor. Taken together, these results suggest that leptin mediates the invasive potential of prostate carcinoma cells, and that this effect is dependent on their androgen sensitivity.Dayanand D. Deo, Ashwin P. Rao, Saideep S. Bose, Allal Ouhtit, Surendra B. Baliga, Shilpa A. Rao, Bruce J. Trock, Rajesh Thouta, Madhwa HG Raj, and Prakash N. Rao© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/259174A compact integrated system-on-chip (SoC) architecture solution for robust, real-time, and on-site genetic analysis has been proposed. This microsystem solution is noise-tolerable and suitable for analyzing the weak fluorescence patterns from a PCR prepared dual-labeled DNA microchip assay. In the architecture, a preceding VLSI differential logarithm microchip is designed for effectively computing the logarithm of the normalized input fluorescence signals. A posterior VLSI artificial neural network (ANN) processor chip is used for analyzing the processed signals from the differential logarithm stage. A single-channel logarithmic circuit was fabricated and characterized. A prototype ANN chip with unsupervised winner-take-all (WTA) function was designed, fabricated, and tested. An ANN learning algorithm using a novel sigmoid-logarithmic transfer function based on the supervised backpropagation (BP) algorithm is proposed for robustly recognizing low-intensity patterns. Our results show that the trained new ANN can recognize low-fluorescence patterns better than an ANN using the conventional sigmoid function.Jaw-Chyng Lue and Wai-Chi Fang© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/846371HTLV-1 causes adult T-cell leukemia (ATL) and HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP). Recombinant envelope glycoprotein is used in production of diagnostic enzyme-linked immunosorbent assay (ELISA) kit. There are some reports that a significant percentage of Iranian HTLV-1 infected patients showed no seroreactivity with MTA-1 peptide, while HTLV-1 had been confirmed by PCR detection methods or ELISA kits containing a cocktail of HTLV-1 specific peptides. This report describes experiments designed to determine whether some discrepancies between ELISA and PCR results could be due to truncation of immunodominant epitopes using immunoassay method. We have cloned the MTA-1 epitope of env gene from HTLV-1 in NotI/NdeI sites of pET22b(+) expression vector. Sequencing analysis of recombinant plasmids revealed an insertion of a cytosine in position 271 causing a stop codon in the MTA-1 protein translation. SDS-PAGE analysis also failed to reveal the presence of the desired protein. Subjects with a mutant HTLV-1 env gene were shown to be seronegative using ELISA, but positive with PCR.Mohammad Reza Abbaszadegan, Narges Jafarzadeh, Mojtaba Sankian, AbdolReza Varasteh, Mahmoud Mahmoudi, Majid Sadeghizadeh, Fatemeh Khatami, and Neema Mehramiz© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2007/82752Marek Osinski, Thomas M. Jovin, and K. Yamamoto© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/165730The equine distal forelimb is a common location of injuries related to mechanical overload. In this study, a two-dimensional model of the musculoskeletal system of the region was developed and applied to kinematic and kinetic data from walking and trotting horses. The forces in major tendons and joint reaction forces were calculated. The components of the joint reaction forces caused by wrapping of tendons around sesamoid bones were found to be of similar magnitude to the reaction forces between the long bones at each joint. This finding highlighted the importance of taking into account muscle-tendon wrapping when evaluating joint loading in the equine distal forelimb.Jonathan S. Merritt, Helen M. S. Davies, Colin Burvill, and Marcus G. Pandy© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/821529Genetic or epigenetic inactivation of the pathway formed by the Fanconi anemia (FA) and BRCA1 proteins occurs in several cancer types, making the affected tumors potentially hypersensitive to DNA cross-linkers and other chemotherapeutic agents. It has been proposed that the inability of FA/BRCA-defective cells to form subnuclear foci of effector proteins, such as FANCD2, can be used as a biomarker to aid individualization of chemotherapy. We show that FANCD2 inactivation not only renders cells sensitive to cross-links, but also oxidative stress, a common effect of cancer therapeutics. Oxidative stress sensitivity does not correlate with FANCD2 or RAD51 foci formation, but associates with increased γH2AX foci levels and apoptosis. Therefore, FANCD2 may protect cells against cross-links and oxidative stress through distinct mechanisms, consistent with the growing notion that the pathway is not linear. Our data emphasize the need for multiple biomarkers, such as γH2AX, FANCD2, and RAD51, to capture all pathway activities.Henning Willers, Lisa A. Kachnic, Chen-Mei Luo, Li Li, Martin Purschke, Kerstin Borgmann, Kathryn D. Held, and Simon N. Powell© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/231904The high incidence of de novo chromosomal aberrations in a population of persons with autism suggests a causal relationship between certain chromosomal aberrations and the occurrence of isolated idiopathic autism. We report on the clinical and cytogenetic findings in a male patient with autism, no physical abnormalities and a de novo balanced (7;16)(p22.1;p16.2) translocation. G-banded chromosomes and fluorescent in situ hybridization (FISH) were used to examine the patient's karyotype as well as his parents'. FISH with specific RP11-BAC clones mapping near 7p22.1 and 16p11.2 was used to refine the location of the breakpoints. This is, in the best of our knowledge, the first report of an individual with autism and this specific chromosomal aberration.Nadia Bayou, Ridha M'rad, Ahlem Belhaj, Hussein Daoud, Lamia Ben Jemaa, Ramzi Zemni, Sylvain Briault, M. Bechir Helayem, and Habiba Chaabouni© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/623475Determining the outline or boundary contour of a two-dimensional object, or the surface of a three-dimensional object poses difficulties particularly when there is substantial measurement noise or uncertainty. By adapting the mathematical approach of stochastic function recovery to this task, it is possible to obtain usable estimates for these boundaries, even in the presence of large amounts of noise. The technique is applied to parametric boundary data and has potential applications in biomedical imaging. It should be considered as one of several techniques to improve the visualization of images.Joseph Kolibal and Daniel Howard© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/562183Insertion-deletion polymorphism (InDeL) is the second most frequent type of genetic variation in the human genome. For the detection of large InDeLs, researchers usually resort to either PCR gel analysis or RFLP, but these are time consuming and dependent on human interpretation. Therefore, a more efficient method for genotyping this kind of genetic variation is needed. In this report, we describe a method that can detect large InDeLs by DHPLC (denaturating high-performance liquid chromatography) using the angiotensin-converting enzyme (ACE) gene I/D polymorphism as a model. The InDeL targeted in this study is characterized by a 288 bp Alu element insertion (I). We used DHPLC at nondenaturating conditions to analyze the PCR product with a flow through the chromatographic column under two different gradients based on the differences between D and I sequences. The analysis described is quick and easy, making this technique a suitable and efficient means for DHPLC users to screen InDeLs in genetic epidemiological studies.Renata Guedes Koyama, Rosa M. R. P. S. Castro, Marco Túlio De Mello, Sergio Tufik, and Mario Pedrazzoli© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/218097We investigate the performance of different classification models and their ability to recognize prostate cancer in an early stage. We build ensembles of classification models in order to increase the classification performance. We measure the performance of our models in an extensive cross-validation procedure and compare different classification models. The datasets come from clinical examinations and some of the classification models are already in use to support the urologists in their clinical work.Joerg D. Wichard, Henning Cammann, Carsten Stephan, and Thomas Tolxdorff© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/852571To study the activation of macrophage and upregulation of costimulatory molecule of CD40 in lipopolysaccharide- (LPS-) induced acute lung injury (ALI) model, and to investigate the pathogenecy of ALI, mice were randomly divided into two groups. ALI model was created by injecting 0.2 mg/kg LPS in phosphate saline (PBS) in trachea. The pathologic changes of mice lungs were observed by HE staining at 24 and 48 hours after LPS treatment, then the alveolar septum damage, abnormal contraction, alveolar space hyperemia, and neutrophils or other inflammatory cells infiltration in the LPS group, but not in the control group, were observed. The expression of CD40 mRNA and CD40 protein molecules were higher in LPS group as compared to the control group by Northern blot and flow cytometry, respectively. Expression of Toll-like receptor-4 (TLR4) in activated macrophage (AMΦ) was higher in LPS group as compared to the control group by RT-PCR. The activation of NF-κB binding to NF-κB consensus oligos increased in LPS group by EMSA in macrophage. The concentrations of TNF-α, MIP-2, and IL-1β cytokines from bronchoalveolar lavage fluid (BALF) were increased significantly in LPS group as compared to the control group by ELISA. The activation of AM and upregulation of costimulatory molecule CD40 induced all kinds of inflammatory cytokines releasing, then led to ALI. Therefore, both of them played vital role in the process of development of ALI.Liang Dong, Shujuan Wang, Ming Chen, Hongjia Li, and Wenxiang Bi© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2007/76514We report a methodology for labeling the GABAC receptor on the surface membrane of intact cells. This work builds upon our earlier work with serotonin-conjugated quantum dots and our studies with PEGylated quantum dots to reduce nonspecific binding. In the current approach, a PEGylated derivative of muscimol was synthesized and attached via an amide linkage to quantum dots coated in an amphiphilic polymer derivative of a modified polyacrylamide. These conjugates were used to image GABAC receptors heterologously expressed in Xenopus laevis oocytes.Ian D. Tomlinson, Hélène A. Gussin, Deborah M. Little, Michael R. Warnement, Haohua Qian, David R. Pepperberg, and Sandra J. Rosenthal© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/683505Gene directed-enzyme prodrug therapy (GDEPT) is an approach for sensitization of tumor cells to an enzymatically activated, otherwise nontoxic, prodrug. Cytochrome P450 2B1 (CYP2B1) metabolizes the prodrugs cyclophosphamide (CPA) and ifosfamide (IFA) to produce the cytotoxic substances phosphoramide mustard and isophosphoramide mustard as well as the byproduct acrolein. We have constructed a retroviral promoter conversion (ProCon) vector for breast cancer GDEPT. The vector allows expression of CYP2B1 from the mouse mammary tumor virus (MMTV) promoter known to be active in the mammary glands of transgenic animals. It is anticipated to be used for the generation of encapsulated viral vector producing cells which, when placed inside or close to a tumor, will act as suppliers of the therapeutic CYP2B1 protein as well as of the therapeutic vector itself. The generated vector was effectively packaged by virus producing cells and allowed the production of high levels of enzymatically active CYP2B1 in infected cells which sensitized them to killing upon treatment with both IFA and CPA. Determination of the respective IC50 values demonstrated that the effective IFA dose was reduced by sixteen folds. Infection efficiencies in vivo were determined using a reporter gene-bearing vector in a mammary cancer cell-derived xenograft tumor mouse model.Reinhard Klein, Bärbel Ruttkowski, Sonja Schwab, Thomas Peterbauer, Brian Salmons, Walter H. Günzburg, and Christine Hohenadl© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/518093Elliptic curve cryptographic algorithms convert input data to unrecognizable encryption and the unrecognizable data back again into its original decrypted form. The security of this form of encryption hinges on the enormous difficulty that is required to solve the elliptic curve discrete logarithm problem (ECDLP), especially over GF(2n), n∈Z+. This paper describes an effective method to find solutions to the ECDLP by means of a molecular computer. We propose that this research accomplishment would represent a breakthrough for applied biological computation and this paper demonstrates that in principle this is possible. Three DNA-based algorithms: a parallel adder, a parallel multiplier, and a parallel inverse over GF(2n) are described. The biological operation time of all of these algorithms is polynomial with respect to n. Considering this analysis, cryptography using a public key might be less secure. In this respect, a principal contribution of this paper is to provide enhanced evidence of the potential of molecular computing to tackle such ambitious computations.Kenli Li, Shuting Zou, and Jin Xv© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/675741We have developed a Windows-based program, ConPath, as a scaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find the longest acyclic graphs. Using end read pairs of fixed-sized mate-pair libraries, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pair, and reports wrong assembly information by validating orientations and gap sizes. We have utilized ConPath in more than 10 microbial genome projects, including Mannheimia succiniciproducens and Vibro vulnificus, where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath. Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures.Pan-Gyu Kim, Hwan-Gue Cho, and Kiejung Park© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/695432Protozoa of the genus Leishmania are causative agents of leishmaniasis, an important health problem in both human and veterinary medicine. Here, we describe a new heat shock protein (HSP) in Leishmania, belonging to the small HSP (sHSP) family in kinetoplastids. The protein is highly conserved in different Leishmania species, showing instead significant divergence with sHSP's from other organisms. The humoral response elicited against this protein during Leishmania infection has been investigated in natural infected humans and dogs, and in experimentally infected hamsters. Leishmania HSP20 is a prominent antigen for canine hosts; on the contrary, the protein seems to be a poor antigen for human immune system. Time-course analysis of appearance of anti-HSP20 antibodies in golden hamsters indicated that these antibodies are produced at late stages of the infection, when clinical symptoms of disease are patent. Finally, the protective efficacy of HSP20 was assessed in mice using a DNA vaccine approach prior to challenge with Leishmania amazonensis.Ana M. Montalvo-Álvarez, Cristina Folgueira, Javier Carrión, Lianet Monzote-Fidalgo, Carmen Cañavate, and Jose M. Requena© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/472719The tree representation as a model for organismal evolution has been in use since before Darwin. However, with the recent unprecedented access to biomolecular data, it has been discovered that, especially in the microbial world, individual genes making up the genome of an organism give rise to different and sometimes conflicting evolutionary tree topologies. This discovery calls into question the notion of a single evolutionary tree for an organism and gives rise to the notion of an evolutionary consensus tree based on the evolutionary patterns of the majority of genes in a genome embedded in a network of gene histories. Here, we discuss an approach to the analysis of genomic data of multiple genomes using bipartition spectral analysis and unsupervised learning. An interesting observation is that genes within genomes that have evolutionary tree topologies, which are in substantial conflict with the evolutionary consensus tree of an organism, point to possible horizontal gene transfer events which often delineate significant evolutionary events.L. Hamel, N. Nahar, M.S. Poptsova, O. Zhaxybayeva, and J.P. Gogarten© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2007/26796Gold-DNA conjugates were investigated in detail by a comprehensive gel electrophoresis study based on 1200 gels. A controlled number of single-stranded DNA of different length was attached specifically via thiol-Au bonds to phosphine-stabilized colloidal gold nanoparticles. Alternatively, the surface of the gold particles was saturated with single stranded DNA of different length either specifically via thiol-Au bonds or by nonspecific adsorption. From the experimentally determined electrophoretic mobilities, estimates for the effective diameters of the gold-DNA conjugates were derived by applying two different data treatment approaches. The first method is based on making a calibration curve for the relation between effective diameters and mobilities with gold nanoparticles of known diameter. The second method is based on Ferguson analysis which uses gold nanoparticles of known diameter as reference database. Our study shows that effective diameters derived from gel electrophoresis measurements are affected with a high error bar as the determined values strongly depend on the method of evaluation, though relative changes in size upon binding of molecules can be detected with high precision. Furthermore, in this study, the specific attachment of DNA via gold-thiol bonds to Au nanoparticles is compared to nonspecific adsorption of DNA. Also, the maximum number of DNA molecules that can be bound per particle was determined.T. Pellegrino, R. A. Sperling, A. P. Alivisatos, and W. J. Parak© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/453590The stable expression of reporter genes in adult stem cells (ASCs) has important applications in stem cell biology. The ability to integrate a noncytotoxic, fluorescent reporter gene into the genome of ASCs with the capability to track ASCs and their progeny is particularly desirable for transplantation studies. The use of fluorescent proteins has greatly aided the investigations of protein and cell function on short-time scales. In contrast, the obtainment of stably expressing cell strains with low variability in expression for studies on longer-time scales is often problematic. We show that this difficulty is partly due to the cytotoxicity of a commonly used reporter, green fluorescent protein (GFP). To avoid GFP-specific toxicity effects during attempts to stably mark a rat hepatic ASC strain and, therefore, obtain stable, long-term fluorescent ASCs, we evaluated cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP), in addition to GFP. Although we were unable to derive stable GFP-expressing strains, stable fluorescent clones (up to 140 doublings) expressing either CFP or YFP were established. When fluorescently marked ASCs were induced to produce differentiated progeny cells, stable fluorescence expression was maintained. This property is essential for studies that track fluorescently marked ASCs and their differentiated progeny in transplantation studies.Rouzbeh R. Taghizadeh and James L. Sherley© 2008, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/GetArticle.aspx?doi=10.1155/2008/768232A talking and singing robot which adaptively learns the vocalization skill by means of an auditory feedback learning algorithm is being developed. The robot consists of motor-controlled vocal organs such as vocal cords, a vocal tract and a nasal cavity to generate a natural voice imitating a human vocalization. In this study, the robot is applied to the training system of speech articulation for the hearing-impaired, because the robot is able to reproduce their vocalization and to teach them how it is to be improved to generate clear speech. The paper briefly introduces the mechanical construction of the robot and how it autonomously acquires the vocalization skill in the auditory feedback learning by listening to human speech. Then the training system is described, together with the evaluation of the speech training by auditory impaired people.Hideyuki Sawada, Mitsuki Kitani, and Yasumori Hayashi© 2008, Hindawi Publishing Corporation. All rights reserved.