bluuebunny/crossref_metadata_2025 huggingface dataset:
Interleukin-8 Production by Human Airway Epithelial Cells in Response to
Pseudomonas aeruginosa
Clinical Isolates Expressing Type a or Type b Flagellins
Authors: Shanks Kathleen K. , Guang Wei , Kim K. Chul , Lillehoj Erik P.
Published: July 2010

Pseudomonas aeruginosa
lung infection is a major cause of morbidity and mortality worldwide.
P. aeruginosa
flagellin, the main structural protein of the flagellar filament, is a virulence factor with proinflammatory activity on respiratory epithelial cells.
P. aeruginosa
bacteria express one of two isoforms of flagellin (type a or b) that differ in their primary amino acid sequences as well as in posttranslational glycosylation. In this study, the distribution of type a and b flagellins among 3
P. aeruginosa
laboratory strains and 14 clinical isolates (1 ulcerative keratitis, 3 cystic fibrosis, and 10 acute pneumonia isolates) was determined, and their abilities to stimulate interleukin-8 (IL-8) production by human airway epithelial cells was compared. By comparison with the PAK (type a) and PAO1 (type b) prototype laboratory strains, 10/14 (71.4%) of clinical isolates expressed type a and 4/14 (28.6%) expressed type b flagellins. Among four cell lines surveyed, BEAS-2B cells were found to give the greatest difference between constitutive and flagellin-stimulated IL-8 production. All 17 flagellins stimulated IL-8 production by BEAS-2B cells (range, 700 to 4,000 pg/ml). However, no discernible differences in IL-8 production were evident when comparing type a versus type b flagellins or flagellins from laboratory versus clinical strains or among the clinical strains.
Immunocapture Enzyme-Linked Immunosorbent Assay for Assessment of
I
n V
itro
Potency of Recombinant Hepatitis B Vaccines
Authors: Shanmugham Rajalakshmi , Thirumeni Nagarajan , Rao Varaprasada Sankarashetty , Pitta Vidyasagar , Kasthuri Saranyarevathy , Singanallur Nagendrakumar Balasubramanian , Lingala Rajendra , Mangamoori Lakshmi Narsu , Villuppanoor Srinivasan Alwar
Published: July 2010

Quantification of hepatitis B surface antigen (HBsAg) or relative
in vitro
potency in the final vaccines is a prerequisite for hepatitis B vaccine batch release. The commercial kit for automated analysis (AxSYM) is expensive, and an alternative is required for the estimation of HBsAg in hepatitis B vaccines. Mouse monoclonal antibodies (MAbs) specific for HBsAg were developed and characterized. One of the monoclonal antibodies (HBs06) was used in development of an immunocapture ELISA (IC-ELISA) as an unlabeled capture antibody and biotin-labeled detection antibody. The IC-ELISA was standardized and validated using experimental hepatitis B vaccine batches with various HBsAg concentrations per dose and commercial vaccines. The vaccine was treated with an alkaline solubilizer to desorb the HBsAg from Algel-adjuvanted vaccines before testing, and the sensitivity of the test was 5 ng/ml. A good correlation could be observed between the HBsAg estimates derived by both formats, except for the higher HBsAg concentration range, where the IC-ELISA format could estimate closer to the actual values than AxSYM. There was a significant correlation between the estimated relative potencies of the two methods. There was lack of correlation between the
in vivo
potency and the relative
in vitro
potency. However, the estimates of IC-ELISA were comparable to the
in vivo
values when compared with the estimates of AxSYM. The IC-ELISA can therefore be considered to be a reliable test for deriving
in vitro
relative potency and antigen concentration in vaccine batches for batch control and release.
Broad-Range 16S rRNA PCR with Cerebrospinal Fluid May Be Unreliable for Management of Postoperative Aseptic Meningitis
Authors: Zarrouk Virginie , Leflon-Guibout Véronique , Robineaux Sébastien , Kalamarides Michel , Nicolas-Chanoine Marie-Hélène , Sterkers Olivier , Fantin Bruno
Published: July 2010

We previously demonstrated that discontinuing presumptive antibiotic treatment in cases of negative conventional cultures is safe and effective for patients with postoperative aseptic meningitis (PAM). Here, we prospectively investigated 32 patients with postoperative meningitis. All 26 patients with PAM diagnosed on the basis of conventional cultures demonstrated negative 16S rRNA PCR results. Our results suggest that the PCR technique does not change PAM management.
Evaluation of a Chromogenic Agar for Detection of Group B Streptococcus in Pregnant Women
Authors: Craven Robin R. , Weber Carol J. , Jennemann Rebecca A. , Dunne W. Michael
Published: July 2010

We compared ChromID Strepto B agar (STRB; bioMérieux, Inc.), a selective and differential medium for group B streptococcus, with culture using neomycin-nalidixic acid agar (NNA) and LIM broth. STRB alone was more sensitive (87.7%) than NNA alone (79.0%), while each had a sensitivity of 100% when used in conjunction with LIM broth.
Axillary Abscess Complicated by Venous Thrombosis: Identification ofStreptococcus pyogenesby 16S PCR
Authors: Kahn Fredrik , Linder Adam , Petersson Ann Cathrine , Christensson Bertil , Rasmussen Magnus
Published: July 2010

We report a case of an axillary abscess withStreptococcus pyogenescomplicated by venous thrombosis. Bacterial etiology and typing were obtained by PCR and sequencing of the 16S rRNA and M-protein genes from abscess material. The bacterium was of serotype M41, and serology indicated that it had expressed procoagulant factors.
Comparison of Broth Microdilution, Agar Dilution, and Etest for Susceptibility Testing of Doripenem against Gram-Negative and Gram-Positive Pathogens
Authors: Amsler K. , Santoro C. , Foleno B. , Bush K. , Flamm R.
Published: July 2010

The susceptibility of 513 clinical isolates to doripenem was determined by broth microdilution, agar dilution, and Etest. Overall agreements for Etest and agar dilution MIC values compared to reference broth microdilution at ±1 log
2
dilution were 88% and 94%, respectively. Etest MIC values demonstrated 98% agreement within ±2 log
2
dilutions compared to the reference broth microdilution method.
Screening of Urine Samples by Flow Cytometry Reduces the Need for Culture
Authors: Jolkkonen Santra , Paattiniemi Eeva-Liisa , Kärpänoja Pauliina , Sarkkinen Hannu
Published: July 2010

Urine samples constitute a large proportion of samples tested in clinical microbiology laboratories. Culturing of the samples is fairly time- and labor-consuming, and most of the samples will yield no growth or insignificant growth. We analyzed the feasibility of the flow cytometry-based UF-500i instrument (Sysmex, Japan) to screen out urine samples with no growth or insignificant growth and reduce the number of samples to be cultured. A total of 1,094 urine specimens sent to our laboratory for culture during 4 months in the spring of 2009 in Lahti, Finland, were included in the study. After culture, all samples were analyzed with the Sysmex UF-500i for bacterial and leukocyte (white blood cell [WBC]) counts. Youden index and closest (0,1) methods were used to determine the cutoff values for bacterial and WBC counts in culture-positive and -negative groups. By flow cytometry, samples considered positive for UTI in culture had bacterial and WBC values that were significantly higher than those for samples considered negative. The flow cytometric screening worked best when both bacterial counts and WBC counts were used with age- and gender-specific cutoff values for all patient groups, excluding patients with urological disease or anomaly. By use of these cutoff values, 5/167 (3.0%) of culture-positive samples were missed by UF-500i and the percentage of samples that did not need to be cultured was 64.5%. Use of the UF-500i instrument is a reliable method for screening out a major part of the UTI-negative samples, significantly diminishing the amount of work required in the microbiology laboratory.
Cerebral Phaeohyphomycosis Caused by
Rhinocladiella mackenziei
in a Woman Native to Afghanistan
Authors: Cristini Alejandro , Garcia-Hermoso Dea , Celard Marie , Albrand Gilles , Lortholary Olivier
Published: July 2010

Rhinocladiella mackenziei
is a recognized cause of endemic cerebral phaeohyphomycosis in the Middle East area. Surgical resection of the abscesses and posaconazole treatment have improved the ominous prognosis of this disease. We describe the case of a native Afghan woman living in France who presented with brain abscesses due to
R. mackenziei.
Macaques Vaccinated with Simian Immunodeficiency Virus SIVmac239Δnef Delay Acquisition and Control Replication after Repeated Low-Dose Heterologous SIV Challenge
Authors: Reynolds Matthew R. , Weiler Andrea M. , Piaskowski Shari M. , Kolar Holly L. , Hessell Ann J. , Weiker Madelyn , Weisgrau Kim L. , León Enrique J. , Rogers W. Eric , Makowsky Robert , McDermott Adrian B. , Boyle Rosanne , Wilson Nancy A. , Allison David B. , Burton Dennis R. , Koff Wayne C. , Watkins David I.
Published: July 2010

An effective human immunodeficiency virus (HIV) vaccine will likely need to reduce mucosal transmission and, if infection occurs, control virus replication. To determine whether our best simian immunodeficiency virus (SIV) vaccine can achieve these lofty goals, we vaccinated eight Indian rhesus macaques with SIVmac239Δnef and challenged them intrarectally (i.r.) with repeated low doses of the pathogenic heterologous swarm isolate SIVsmE660. We detected a significant reduction in acquisition of SIVsmE660 in comparison to that for naïve controls (log rank test;
P
= 0.023). After 10 mucosal challenges, we detected replication of the challenge strain in only five of the eight vaccinated animals. In contrast, seven of the eight control animals became infected with SIVsmE660 after these 10 challenges. Additionally, the SIVsmE660-infected vaccinated animals controlled peak acute virus replication significantly better than did the naïve controls (Mann-Whitney U test;
P
= 0.038). Four of the five SIVsmE660 vaccinees rapidly brought virus replication under control by week 4 postinfection. Unfortunately, two of these four vaccinated animals lost control of virus replication during the chronic phase of infection. Bulk sequence analysis of the circulating viruses in these animals indicated that recombination had occurred between the vaccine and challenge strains and likely contributed to the increased virus replication in these animals. Overall, our results suggest that a well-designed HIV vaccine might both reduce the rate of acquisition and control viral replication.
A Disulfide-Bonded Dimer of the Core Protein of Hepatitis C Virus Is Important for Virus-Like Particle Production
Authors: Kushima Yukihiro , Wakita Takaji , Hijikata Makoto
Published: July 2010

Hepatitis C virus (HCV) core protein forms the nucleocapsid of the HCV particle. Although many functions of core protein have been reported, how the HCV particle is assembled is not well understood. Here we show that the nucleocapsid-like particle of HCV is composed of a disulfide-bonded core protein complex (dbc-complex). We also found that the disulfide-bonded dimer of the core protein (dbd-core) is formed at the endoplasmic reticulum (ER), where the core protein is initially produced and processed. Mutational analysis revealed that the cysteine residue at amino acid position 128 (Cys128) of the core protein, a highly conserved residue among almost all reported isolates, is responsible for dbd-core formation and virus-like particle production but has no effect on the replication of the HCV RNA genome or the several known functions of the core protein, including RNA binding ability and localization to the lipid droplet. The Cys128 mutant core protein showed a dominant negative effect in terms of HCV-like particle production. These results suggest that this disulfide bond is critical for the HCV virion. We also obtained the results that the dbc-complex in the nucleocapsid-like structure was sensitive to proteinase K but not trypsin digestion, suggesting that the capsid is built up of a tightly packed structure of the core protein, with its amino (N)-terminal arginine-rich region being concealed inside.
The Clinically Approved Proteasome Inhibitor PS-341 Efficiently Blocks Influenza A Virus and Vesicular Stomatitis Virus Propagation by Establishing an Antiviral State
Authors: Dudek Sabine Eva , Luig Christina , Pauli Eva-Katharina , Schubert Ulrich , Ludwig Stephan
Published: July 2010

Recently it has been shown that the proinflammatory NF-κB pathway promotes efficient influenza virus propagation. Based on these findings, it was suggested that NF-κB blockade may be a promising approach for antiviral intervention. The classical virus-induced activation of the NF-κB pathway requires proteasomal degradation of the inhibitor of NF-κB, IκB. Therefore, we hypothesized that inhibition of proteasomal IκB degradation should impair influenza A virus (IAV) replication. We chose the specific proteasome inhibitor PS-341, which is a clinically approved anticancer drug also known as Bortezomib or Velcade. As expected, PS-341 treatment of infected A549 cells in a concentration range that was not toxic resulted in a significant reduction of progeny virus titers. However, we could not observe the proposed suppression of NF-κB-signalingin vitro. Rather, PS-341 treatment resulted in an induction of IκB degradation and activation of NF-κB as well as the JNK/AP-1 pathway. This coincides with enhanced expression of antiviral genes, such as interleukin-6 and, most importantly, MxA, which is a strong interferon (IFN)-induced suppressor of influenza virus replication. This suggests that PS-341 may act as an antiviral agent via induction of the type I IFN response. Accordingly, PS-341 did not affect virus titers in Vero cells, which lack type I IFN genes, but strongly inhibited replication of vesicular stomatitis virus (VSV), a highly IFN-sensitive pathogen. Thus, we conclude that PS-341 blocks IAV and VSV replication by inducing an antiviral state mediated by the NF-κB-dependent expression of antivirus-acting gene products.
High Variability and Rapid Evolution of a Nanovirus
Authors: Grigoras Ioana , Timchenko Tatiana , Grande-Pérez Ana , Katul Lina , Vetten Heinrich-Josef , Gronenborn Bruno
Published: July 2010

Nanoviruses are multipartite single-stranded DNA (ssDNA) plant viruses that cause important diseases of leguminous crops and banana. Little has been known about the variability and molecular evolution of these viruses. Here we report on the variability of faba bean necrotic stunt virus (FBNSV), a nanovirus from Ethiopia. We found mutation frequencies of 7.52 × 10
−4
substitutions per nucleotide in a field population of the virus and 5.07 × 10
−4
substitutions per nucleotide in a laboratory-maintained population derived thereof. Based on virus propagation for a period of more than 2 years, we determined a nucleotide substitution rate of 1.78 × 10
−3
substitutions per nucleotide per year. This high molecular evolution rate places FBNSV, as a representative of the family
Nanoviridae
, among the fastest-evolving ssDNA viruses infecting plants or vertebrates.
All Three Domains of the Hepatitis C Virus Nonstructural NS5A Protein Contribute to RNA Binding
Authors: Foster Toshana L. , Belyaeva Tamara , Stonehouse Nicola J. , Pearson Arwen R. , Harris Mark
Published: July 2010

The hepatitis C virus (HCV) nonstructural protein NS5A is critical for viral genome replication and is thought to interact directly with both the RNA-dependent RNA polymerase, NS5B, and viral RNA. NS5A consists of three domains which have, as yet, undefined roles in viral replication and assembly. In order to define the regions that mediate the interaction with RNA, specifically the HCV 3′ untranslated region (UTR) positive-strand RNA, constructs of different domain combinations were cloned, bacterially expressed, and purified to homogeneity. Each of these purified proteins was probed for its ability to interact with the 3′ UTR RNA using filter binding and gel electrophoretic mobility shift assays, revealing differences in their RNA binding efficiencies and affinities. A specific interaction between domains I and II of NS5A and the 3′ UTR RNA was identified, suggesting that these are the RNA binding domains of NS5A. Domain III showed lowin vitroRNA binding capacity. Filter binding and competition analyses identified differences between NS5A and NS5B in their specificities for defined regions of the 3′ UTR. The preference of NS5A, in contrast to NS5B, for the polypyrimidine tract highlights an aspect of 3′ UTR RNA recognition by NS5A which may play a role in the control or enhancement of HCV genome replication.
Identification of a gp41 Core-Binding Molecule with Homologous Sequence of Human TNNI3K-Like Protein as a Novel Human Immunodeficiency Virus Type 1 Entry Inhibitor
Authors: Zhu Yun , Lu Lu , Xu Liling , Yang Hengwen , Jiang Shibo , Chen Ying-Hua
Published: July 2010

Human immunodeficiency virus type 1 (HIV-1) gp41 plays a critical role in the viral fusion process, and its N- and C-terminal heptad repeat domains serve as important targets for developing anti-HIV-1 drugs, like T-20 (generic name, enfuvirtide; brand name, Fuzeon). Here, we conducted a yeast two-hybrid screening on a human bone marrow cDNA library using the recombinant soluble gp41 ectodomain as the bait and identified a novel gp41 core-binding molecule, designated P20. P20 showed no homology with a current HIV fusion inhibitor, T-20, but had sequence homology to a human protein, troponin I type 3 interacting kinase (TNNI3K)-like protein. While it could bind to the six-helix bundle core structure formed by the N- and C-terminal heptad repeats, P20 did not interrupt the formation of the six-helix bundle. P20 was effective in blocking HIV-1 Env-mediated syncytium formation and inhibiting infection by a broad spectrum of HIV-1 strains with distinct subtypes and coreceptor tropism, while it was ineffective against other enveloped viruses, such as vesicular stomatitis virus and influenza A virus. P20 exhibited no significant cytotoxicity to the CD4
+
cells that were used for testing antiviral activity. Among the 11 P20 mutants, four analogous peptides with a common motif (WGRLEGRRT) exhibited significantly reduced anti-HIV-1 activity, suggesting that this region is the critical active site of P20. Therefore, this peptide can be used as a lead for developing novel HIV fusion inhibitors and as a probe for studying the membrane-fusogenic mechanism of HIV.
Alpha/Beta Interferon (IFN-α/β)-Independent Induction of IFN-λ1 (Interleukin-29) in Response to Hantaan Virus Infection
Authors: Stoltz Malin , Klingström Jonas
Published: July 2010

Type III interferons ([IFNs]IFN-λ and interleukin-28 and -29 [IL-28/29]) are recently recognized cytokines with innate antiviral effects similar to those of type I IFNs (IFN-α/β). Like IFN-α/β, IFN-λ-expression can be induced by viruses, and it is believed that type I and III IFNs are regulated in the same manner. Hantaviruses are weak IFN-α/β inducers and have surprisingly been shown to activate IFN-α/β-independent IFN-stimulated gene (ISG) expression. Here, we show that in Hantaan virus (HTNV)-infected human epithelial A549 cells, induction of IFN-λ1 preceded induction of MxA and IFN-β by 12 and 24 h, respectively, and IFN-α was not induced at all. Furthermore, induction of IFN-λ1 and MxA was observed in HTNV-infected African green monkey epithelial Vero E6 cells, a cell line that cannot produce type I IFNs, clearly showing that HTNV can induce IFN-λ1 and ISGs in the complete absence of IFN-α/β. In HTNV-infected human fibroblast MRC-5 cells, which lack the IFN-λ receptor, induction of MxA coincided in time with IFN-β-induction. UV-inactivated HTNV did not induce any IFNs or MxA in any cell line, showing that activation of IFN-λ1 is dependent on replicating virus. Induction of both IFN-β and IFN-λ1 in A549 cells after poly(I:C)-stimulation was strongly inhibited in HTNV-infected cells, suggesting that HTNV can inhibit signaling pathways used to simultaneously activate types I and III IFNs. In conclusion, we show that HTNV can cause type I IFN-independent IFN-λ1 induction and IFN-λ1-specific ISG induction. Importantly, the results suggest the existence of specific signaling pathways that induce IFN-λ1 without simultaneous type I IFN induction during virus infection.
Stress-Inducible Alternative Translation Initiation of Human Cytomegalovirus Latency Protein pUL138
Authors: Grainger Lora , Cicchini Louis , Rak Michael , Petrucelli Alex , Fitzgerald Kerry D. , Semler Bert L. , Goodrum Felicia
Published: July 2010

We have previously characterized a 21-kDa protein encoded byUL138(pUL138) as a viral factor inherent to low-passage strains of human cytomegalovirus (HCMV) that is required for latent infectionin vitro. pUL138 is encoded on 3.6-, 2.7-, and 1.4-kb 3′ coterminal transcripts that are produced during productive and latent infections. pUL138 is encoded at the 3′ end of each transcript and is preceded by an extensive 5′ sequence (∼0.5 to 2.5 kb) containing several putative open reading frames (ORFs). We determined that three putative ORFs upstream ofUL138(UL133,UL135, andUL136) encode proteins. TheUL138transcripts are polycistronic, such that each transcript expresses pUL138 in addition to the most-5′ ORF. The upstream coding sequences (CDS) present a significant challenge for the translation of pUL138 in mammalian cells. We hypothesized that sequences 5′ ofUL138mediate translation initiation of pUL138 by alternative strategies. Accordingly, a 663-nucloetide (nt) sequence overlapping theUL136CDS supported expression of a downstream cistron in a bicistronic reporter system. We did not detect cryptic promoter activity or RNA splicing events that could account for downstream cistron expression. These data are consistent with the sequence element functioning as an internal ribosome entry site (IRES). Interestingly, pUL138 expression from the 3.6- and 2.7-kb transcripts was induced by serum stress, which concomitantly inhibited normal cap-dependent translation. Our work suggests that an alternative and stress-inducible strategy of translation initiation ensures expression of pUL138 under a variety of cellular contexts. TheUL138polycistronic transcripts serve to coordinate the expression of multiple proteins, including a viral determinant of HCMV latency.
Genetic and Phenotypic Characterization of GII-4 Noroviruses That Circulated during 1987 to 2008
Authors: Yang Yang , Xia Ming , Tan Ming , Huang Pengwei , Zhong Weiming , Pang Xiao Li , Lee Bonita E. , Meller Jarek , Wang Tao , Jiang Xi
Published: July 2010

The predominance and continual emergence of new variants in GII-4 noroviruses (NVs) in recent years have raised questions about the role of host immunity and histo-blood group antigens (HBGAs) in NV evolution. To address these questions, we performed a genetic and phenotypic characterization of GII-4 variants circulating in the past decade (1998 to 2008). Ninety-three GII-4 sequences were analyzed, and of them, 16 strains representing 6 genetic clusters were selected for further characterization. The HBGA binding properties were determined by both saliva- and oligosaccharide-binding assays using P particles as a model of NV capsid. The antigenic properties were also examined by enzyme immunoassay (EIA), Western blot analysis, and receptor blocking assay, using P-particle-specific antibodies from immunized mice and GII-4 virus-infected patients. Our results showed that 15 of the 16 GII-4 viruses bound to saliva of all A, B, and O secretors. Oligosaccharide binding assays yielded largely consistent results, although the binding affinities to some oligosaccharides varied among some strains. The only nonbinder had a mutation in the binding site. While antigenic variations were detected among the 16 strains, significant cross-blocking on the HBGA binding was also noted. Sequence alignment revealed high conservation of HBGA binding interfaces with some variations in adjacent regions. Taken together, our data suggested that the ability of GII-4 to recognize different secretor HBGAs persisted over the past decade, which may explain the predominance of GII-4 over other genotypes. Our data also indicated that both the host immunity and HBGAs play a role in NV evolution. While host immunity may continue driving NV for antigenic change, the functional selection by the HBGAs tends to lock the architecture of the capsid/HBGA interfaces and allows only limited variations outside the HBGA binding sites. A potential outcome of such counterselection between theses two factors in NV evolution is discussed.
LEAVING AN UNKNOWN MAZE USING AN ERROR-PRONE COMPASS
Authors: KAMPHANS TOM , LANGETEPE ELMAR
Published: July 2010

Imagine you are trapped in a maze of caves. All you have is an old rusty compass and barely enough light to read it. How much inaccuracy can you allow to ensure that you can leave the maze? Or you are walking in a maze of hedgerows that are on the whole orthogonal. Can you find the exit by counting left and right turns?

We consider the problem of escaping from an unknown polygonal maze under limited resources and errors in inputs and motion. It is well known that the Pledge algorithm always finds a path out of an unknown maze without any means of orientation—provided that such a path exists—but it relies on fact that inputs and motions are correct.
GUARDING A POLYGON FROM TWO NEARLY-OPPOSITE DIRECTIONS
Authors: BRASS PETER , NA HYEON-SUK , SHIN CHAN-SU
Published: July 2010

In this paper, we study a variant of the classical art-gallery problem, in which we require that each point of the art gallery is observed by two guards from nearly-opposite directions, ideally from front and back. We call a polygon P α-guarded by a set G of guards if every point p in P is visible from two guards g1,g2 in G satisfying α ≤ ∠g1pg2 ≤ π.

We show that any simple n-gon is ⅔π-guarded by its n vertex guards, and there are simple n-gons that require at least n guards. Any simple n-gon can be (π – δ)-guarded by [Formula: see text] guards, and there are simple n-gons that require at least [Formula: see text] guards in any guard placement.

We prove that the region of a simple n-gon that is α-guarded by k guards can have Θ(nk + k4) complexity in the worst case. Given simple n-gon P and k guard positions, we can decide for a fixed 0 < α < π whether P is α-guarded in O((nk2 + k4) log 2 nk) time and find the largest α < π for which P is α-guarded in O((nk2 + k4) log 6 nk) time.
ATRIPPI: AN ATOM-RESIDUE PREFERENCE SCORING FUNCTION FOR PROTEIN–PROTEIN INTERACTIONS
Authors: LIU KANG-PING , HSU KAI-CHENG , HUANG JHANG-WEI , CHANG LU-SHIAN , YANG JINN-MOON
Published: July 2010

We present an ATRIPPI model for analyzing protein–protein interactions. This model is a 167-atom-type and residue-specific interaction preferences with distance bins derived from 641 co-crystallized protein–protein interfaces. The ATRIPPI model is able to yield physical meanings of hydrogen bonding, disulfide bonding, electrostatic interactions, van der Waals and aromatic–aromatic interactions. We applied this model to identify the native states and near-native complex structures on 17 bound and 17 unbound complexes from thousands of decoy structures. On average, 77.5% structures (155 structures) of top rank 200 structures are closed to the native structure. These results suggest that the ATRIPPI model is able to keep the advantages of both atom–atom and residue–residue interactions and is a potential knowledge-based scoring function for protein–protein docking methods. We believe that our model is robust and provides biological meanings to support protein–protein interactions.
BEE COLONY OPTIMIZATION WITH LOCAL SEARCH FOR TRAVELING SALESMAN PROBLEM
Authors: WONG LI-PEI , LOW MALCOLM YOKE HEAN , CHONG CHIN SOON
Published: July 2010

Many real world industrial applications involve the Traveling Salesman Problem (TSP), which is a problem that finds a Hamiltonian path with minimum cost. Examples of problems that belong to this category are transportation routing problem, scan chain optimization and drilling problem in integrated circuit testing and production. This paper presents a Bee Colony Optimization (BCO) algorithm for symmetrical TSP. The BCO model is constructed algorithmically based on the collective intelligence shown in bee foraging behaviour. The algorithm is integrated with a fixed-radius near neighbour 2-opt (FRNN 2-opt) heuristic to further improve prior solutions generated by the BCO model. To limit the overhead incurred by the FRNN 2-opt, a frequency-based pruning strategy is proposed. The pruning strategy allows only a subset of the promising solutions to undergo local optimization. Experimental results comparing the proposed BCO algorithm with existing approaches on a set of benchmark problems are presented. For 84 benchmark problems, the BCO algorithm is able to obtain an overall average solution quality of 0.31% from known optimum. The results also show that it is comparable to other algorithms such as Ant Colony Optimization and Particle Swarm Optimization.
Synthetic porphyrins bearing β-propionate chains as photosensitizers for photodynamic therapy
Authors: Pereira Nelson , Serra Arménio C. , Pineiro Marta , Gonsalves António M. d'A. Rocha , Abrantes Margarida , Laranjo Mafalda , Botelho Filomena
Published: July 2010

Porphyrins with different numbers of β-propionate chains mimicking natural porphyrins were prepared via the 2+2 MacDonald type approach. Photodynamic activity against WiDr colon adenocarcinoma cells showed that activity is related to the number of β-propionate chains, with the derivatives with two carboxylic groups showing higher activity.
Molecular Analysis of Plasma DNA for the Early Detection of Lung Cancer by Quantitative Methylation-Specific PCR
Authors: Ostrow Kimberly Laskie , Hoque Mohammad O. , Loyo Myriam , Brait Marianna , Greenberg Alissa , Siegfried Jill M. , Grandis Jennifer R. , Gaither Davis Autumn , Bigbee William L. , Rom William , Sidransky David
Published: July 2010

Purpose: Aberrant promoter hypermethylation of tumor suppressor genes is a promising marker for lung cancer detection. We investigated the likelihood of detecting aberrant DNA methylation of tumor suppressor genes in plasma samples of patients with abnormalities of the lung detected upon computed tomography (CT) scan.

Experimental Design: In a small evaluation cohort, four gene promoters (DCC, Kif1a, NISCH, and Rarb) were found to be methylated with increased frequency in samples from cancer patients specifically. We then examined DNA from 93 plasma samples from patients with abnormal findings in the lung detected upon CT scan for aberrant methylation of these four gene promoters by quantitative fluorogenic real-time PCR. The patients were divided into two groups, ground glass opacity (n = 23) and cancerous tumors (n = 70). Plasma DNA from age-matched nodule-free individuals were used as controls (n = 80).

Results: In plasma, 73% of patients with cancerous tumors showed methylation of at least one gene with a specificity of 71% (P = 0.0001). Only 22% patients with ground glass opacity exhibited methylation of at least one gene. When smoking history was taken into account, 72% of cancer patients with no smoking history or those who smoked <20 pack-years showed methylation of at least one gene with 100% specificity (P = 0.05) when compared with matched controls. Among heavy smokers with 20+ pack-years of smoking history, 30% of the control group and 73% of the patients with cancerous tumors showed methylation (P = 0.0001).

Conclusions: These biomarkers can distinguish between cancerous and noncancerous abnormal CT findings. Clin Cancer Res; 16(13); 3463–72. ©2010 AACR.
BRCA1 Loss Preexisting in Small Subpopulations of Prostate Cancer Is Associated with Advanced Disease and Metastatic Spread to Lymph Nodes and Peripheral Blood
Authors: Bednarz Natalia , Eltze Elke , Semjonow Axel , Rink Michael , Andreas Antje , Mulder Lennart , Hannemann Juliane , Fisch Margit , Pantel Klaus , Weier Heinz-Ulrich G. , Bielawski Krzysztof P. , Brandt Burkhard
Published: July 2010

Purpose: A preliminary study performed on a small cohort of multifocal prostate cancer (PCa) detected BRCA1 allelic imbalances among circulating tumor cells (CTC). The present analysis was aimed to elucidate the biological and clinical roles of BRCA1 losses in metastatic spread and tumor progression in PCa patients.

Experimental Design: To map molecular progression in PCa outgrowth, we used fluorescence in situ hybridization analysis of primary tumors and lymph node sections, and CTCs from peripheral blood.

Results: We found that 14% of 133 tested patients carried monoallelic BRCA1 loss in at least one tumor focus. Extended molecular analysis of chr17q revealed that this aberration was often a part of larger cytogenetic rearrangement involving chr17q21 accompanied by allelic imbalance of the tumor suppressor gene PTEN and lack of BRCA1 promoter methylation. The BRCA1 losses correlated with advanced T stage (P < 0.05), invasion to pelvic lymph nodes (P < 0.05), as well as biochemical recurrence (P < 0.01). Their prevalence was twice as high within 62 lymph node metastases (LNM) as in primary tumors (27%, P < 0.01). The analysis of 11 matched primary PCa-LNM pairs confirmed the suspected transmission of genetic abnormalities between these two sites. In four of seven patients with metastatic disease, BRCA1 losses appeared in a minute fraction of cytokeratin- and vimentin-positive CTCs.

Conclusions: Small subpopulations of PCa cells bearing BRCA1 losses might be one confounding factor initiating tumor dissemination and might provide an early indicator of shortened disease-free survival. Clin Cancer Res; 16(13); 3340–8. ©2010 AACR.
Mutation of SDHB is a Cause of Hypoxia-Related High-Altitude Paraganglioma
Authors: Cerecer-Gil Nidia Y. , Figuera Luis E. , Llamas Francisco J. , Lara Mauricio , Escamilla José G. , Ramos Ruben , Estrada Gerardo , Hussain A. Karim , Gaal José , Korpershoek Esther , de Krijger Ronald R. , Dinjens Winand N.M. , Devilee Peter , Bayley Jean Pierre
Published: July 2010

Purpose: Paragangliomas of the head and neck are neuroendocrine tumors and are associated with germ line mutations of the tricarboxylic acid cycle–related genes SDHB, SDHC, SDHD, and SDHAF2. Hypoxia is important in most solid tumors, and was directly implicated in tumorigenesis over 40 years ago when it was shown that dwelling at high altitudes increases the incidence of carotid body hyperplasia and paragangliomas. Although recent research has now elucidated several pathways of hypoxia in paragangliomas, nothing is currently known of the genetics or of gene-environment interactions in high-altitude paraganglioma. We postulated that SDH mutations might play a role in these tumors.

Experimental Design: Patients from a Mexican family, originating and resident in Guadalajara, were tested for mutations of SDHD, and subsequently, for mutations of SDHB followed by immunohistochemical confirmation of SDHB loss.

Results: Two patients, born and resident at altitudes of between 1,560 and 2,240 m, were found to have head and neck paragangliomas, including a remarkably aggressive recurrent tumor. Mutation analysis identified a pathogenic missense mutation in exon 7 of SDHB, c.689G>A, p.Arg230His, and loss of the SDHB protein was confirmed by immunohistochemistry.

Conclusions: This is the first report of a SDH gene mutation in paraganglioma at high altitude. A rapidly recurrent head and neck paraganglioma is a very rare finding in an SDH mutation carrier, suggesting a gene-environment interaction. Neither patient showed evidence of sympathetic paraganglioma. Clin Cancer Res; 16(16); 4148–54. ©2010 AACR.
Imbalance of Matrix Metalloproteinases/Tissue Inhibitor of Metalloproteinase-1 and Loss of Fibronectin Expression in Patients with Congestive Heart Failure
Authors: Yang Da-chun , Ma Shuang-tao , Tan Yan , Chen Yi-hua , Li De , Tang Bing , Chen Jin-song , Su Xiao-hua , Li Gang , Zhang Xin , Yang Yong-jian
Published: July 2010

Objective: Previous studies have demonstrated that an imbalance of matrix metalloproteinases (MMPs)/tissue inhibitors of metalloproteinase-1 (TIMP-1) and a loss of fibronectin are associated with postmyocardial infarction remodeling in rats. The present study was designed to examine this issue in patients with congestive heart failure (CHF). Methods: We measured plasma levels and the cardiac protein expression of MMPs/TIMP-1 and fibronectin in 39 patients with CHF and 38 controls. Results: Plasma levels of MMP-2, MMP-3, and MMP-9 tended to be higher in patients with CHF (NYHA II: 276 ± 18, 613 ± 118, and 245 ± 43 µg/l, respectively; NYHA III: 302 ± 20, 850 ± 132, and 310 ± 39 µg/l, respectively; NYHA IV: 367 ± 15, 998 ± 99, and 392 ± 27 µg/l, respectively) than in controls (213 ± 23, 485 ± 102, and 158 ± 31 µg/l, respectively), while the plasma TIMP-1 level tended to be lower in patients with CHF (NYHA II: 126 ± 12 µg/l, NYHA III: 83 ± 11 µg/l, and NYHA IV: 61 ± 12 µg/l) than in controls (208 ± 15 µg/l). Interestingly, the changes in protein expression of MMPs/TIMP-1 were consistent with their plasma concentration. Furthermore, the fibronectin level in the patients with CHF was significantly lower than in the controls. Conclusions: These data suggest that human CHF is associated with an imbalance of MMPs/TIMP-1 and a concurrent loss of fibronectin.
Multimodality Imaging Reveals a Gradual Increase in Matrix Metalloproteinase Activity at Aneurysmal Lesions in Live Fibulin-4 Mice
Authors: Kaijzel Eric L. , van Heijningen Paula M. , Wielopolski Piotr A. , Vermeij Marcel , Koning Gerben A. , van Cappellen Wiggert A. , Que Ivo , Chan Alan , Dijkstra Jouke , Ramnath Natasja W.M. , Hawinkels Lukas J.A.C. , Bernsen Monique R. , Löwik Clemens W.G.M. , Essers Jeroen
Published: July 2010

Background—

We imaged the protease activity of matrix metalloproteinases (MMPs) upregulated during aneurysm formation, using protease-activatable near-infrared fluorescence probes. We tested whether these protease-activatable sensors can directly report the in vivo activity of the key biomarkers in aneurysm, using our genetically modified fibulin-4 mouse models for aneurysm formation. Mice homozygous for the fibulin-4 reduced-expression allele (fibulin-4
R/R
) show dilatation of the ascending aorta and a tortuous, stiffened aorta resulting from disorganized elastic fiber networks. Strikingly, even a moderate reduction in expression of fibulin-4 in the heterozygous fibulin-4
+/R
mice occasionally results in modest aneurysm formation.

Methods and Results—

Aorta transcriptome and protein expression analysis of fibulin-4
+/R
and fibulin-4
R/R
animals identified excessive transforming growth factor-β signaling as the critical event in the pathogenesis of aneurysm formation. To determine whether a perturbed elastin lamellar structure arose from induction of transforming growth factor-β-regulated MMPs, we performed gelatin zymography and used a protease-activatable near-infrared fluorescence probe to monitor and quantify MMP upregulation in animals, using various in vivo optical imaging modules and coregistration of the fluorescence signal with CT images of the same animals. Gelatin zymography demonstrated a significant increase in the presence of the active form of MMP-9 in the aortic arch of fibulin-4
R/R
mice. In vivo analysis of MMP upregulation using the near-infrared fluorescence probe and subsequent isosurface concentration mapping from reconstructed tomographic images from fibulin-4
+/R
and fibulin-4
R/R
mice revealed a graded increase in activation of MMPs within the aneurysmal lesions.

Conclusions—

We aimed to develop molecular imaging procedures for faster, earlier, and easier recognition of aortic aneurysms. We show that in vivo coregistration of MMP activity by noninvasive tomographic imaging methods allows the detection of increased MMP activity, even before the aneurysm has actually formed.
Balancing on Land and at Sea: Do States Ally against the Leading Global Power?
Authors: Levy Jack S. , Thompson William R.
Published: July 2010

Scholars often interpret balance of power theory to imply that great powers almost always balance against the leading power in the system, and they conclude that the absence of a counterbalancing coalition against the historically unprecedented power of the United States after the end of the Cold War is a puzzle for balance of power theory. They are wrong on both counts. Balance of power theory is not universally applicable. Its core propositions about balancing strategies and the absence of sustained hegemonies apply to the European system and perhaps to some other autonomous continental systems but not to the global maritime system. Sea powers are more interested in access to markets than in territorial aggrandizement against other great powers. Consequently, patterns of coalition formation have been different in the European system and in the global maritime system during the last five centuries. An empirical analysis demonstrates that counterhegemonic balancing is frequent in Europe but much less frequent in the global system. Higher concentrations of power in the global system lead to fewer and smaller rather than more frequent and larger balancing coalitions, as well as to more frequent and larger alliances with the leading sea power than against it.
Getting What You Want: Positive Inducements in International Relations
Authors: Nincic Miroslav
Published: July 2010

Positive inducements as a strategy for dealing with regimes that challenge core norms of international behavior and the national interests of the United States (“renegade regimes”) contain both promises and pitfalls. Such inducements, which include policy concessions and economic favors, can serve two main purposes: (1) arranging a beneficial quid pro quo with the other side, and (2) catalyzing, via positive engagement, a restructuring of interests and preferences within the other side's politico-economic system (such that quid pro quos become less and less necessary). The conditions for progress toward either purpose can vary, as can the requirements for sufficient and credible concessions on both sides and the obstacles in the way of such concessions. For renegade regimes, a primary consideration involves the domestic purposes that internationally objectionable behavior can serve. An examination of the cases of North Korea, Iran, and Libya finds that negative pressures have been relatively ineffective, suggesting that more attention should be given to the potential for positive inducements to produce better outcomes.
Rembrandt, de verwarde bruidegom
Authors: Groeneweg Irene
Published: July 2010

The signature on Rembrandt's little sketch of Saskia in silver point on parchment, bearing the date '8 juni 1633', has long been a source of puzzlement. For how can Rembrandt's remarks - that Saskia was his wife and that on June 8 of that year the couple had been married for three days - be reconciled with the true date of their wedding, June 22 1634, recorded in the register of marriages of Sint-Annaparochie in Friesland? There is however an explanation for the mystifying caption. First, Rembrandt had written that Saskia was 21 years old. Her baptism was registered on August 2 1612, so that she was still only 20 in June 1633. Furthermore, it was compulsory by law to give notice of a marriage, after registration at the town hall and prior to the actual ceremony, by means of a public announcement in the next three weeks. The banns were usually called in church on three successive Sundays. Rembrandt's and Saskia's first bann was called in the church at Sint-Annaparochie on Sunday June 8 1634 - according to the Julian calendar still used in Friesland at that time, which was ten days behind the Gregorian calendar adhered to in Holland. On June 22, the Sunday of the third announcement, their marriage was solemnized. In the seventeenth century, however, many people regarded the day on which the banns were first called as the actual wedding-day, for the betrothed couple could no longer change their minds. Rembrandt and Saskia, then, regarded their wedding-day as June 8 1634 - according to the Frisian calendar. The caption to the sketch thus correctly reads: This is my 21-year-old wife, drawn three days after our wedding-day, and that was on June 8.
Knabe im Atelier und Bücherstilleben, zwei frühe Gemälde von Jan Lievens und ihr Leidener Kontext: Rembrandt, Jan Davidz. de Heem, Pieter Codde
Authors: Schnackenburg Bernhard
Published: July 2010

A painting entitled Le jeune Dessinateur (the young draughtsman), identified in 1932 by Hans Schneider as an early work by Jan Lievens and hung in the Louvre together with Rembrandt, should still, according to prevailing scholarly opinion, be attributed to the much younger Wallerent Vaillant on the basis of a reproduction engraving with his address. It was made after Vaillant and Michael Sweerts had come across the more than 30-year old Lievens painting in about 1660 which inspired them to make variants of their own in the style of their times - variants which Vaillant also published as engravings. This important consequence underlines the status of an unrecognised major work by the young Jan Lievens, a work which in terms of content and form has much to tell us about painting in Leiden around 1628. The curious iconography (the boy is not drawing, but studying drawings, in keeping with Schneider's understanding of the title, Knabe in Atelier (Boy in the Studio), is found only in Pieter Codde's work of that period. Codde owned many works by Leiden painters, prompting Abraham Bredius to suggest as early as 1888 that this Amsterdam painter worked in Leiden for a while. A studio prop in the form of a plaster cast of the infant Jesus from Michelangelo's Bruges Madonna casts a new light on Lievens' interest in the great exemplars of classical art, an interest which Constantijn Huygens failed to perceive when he visited the studio. Lievens had depicted the figure before, in oblique perspective ; it was evidently important for the training of his ability to render three-dimensionality. The group of studio plaster casts is related to a hitherto anonymous Leiden Still Life with Books dating from about 1628, in the Alte Pinakothek, Munich. Discussed earlier in connection with Lievens, this still life is now assigned to Lievens himself, an attribution which is supported by additional arguments. The choice of motif and monochrome colouring has aspects in common with the Vanitas and still lifes with books painted by Jan Davidz. de Heem during the same period and endorsing, with new arguments, his connection with Lievens' and Rembrandt's circle. Lievens' Boy in the Studio, finally, is of significance for the interpretation of Rembrandt's Young Painter in the Studio in Boston, painted at the same time. The two pictures would appear to be linked by antithetical basic statements and art education.