bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments
Authors: Slater Alex W. , Castellanos Javier I. , Sippl Manfred J. , Melo Francisco
Published: October 2012

Motivation: Pairwise alignment of protein structures is a fundamental task in structural bioinformatics. There are numerous computer programs in the public domain that produce alignments for a given pair of protein structures, but the results obtained by the various programs generally differ substantially. Hence, in the application of such programs the question arises which of the alignment programs are the most trustworthy in the sense of overall performance, and which programs provide the best result for a given pair of proteins. The major problem in comparing, evaluating and judging alignment results is that there is no clear notion of the optimality of an alignment. As a consequence, the numeric criteria and scores reported by the individual structure alignment programs are largely incomparable.

Results: Here we report on the development and application of a new approach for the evaluation of structure alignment results. The method uses the translation vector and rotation matrix to generate the superposition of two structures but discards the alignment reported by the individual programs. The optimal alignment is then generated in standardized form based on a suitably implemented dynamic programming algorithm where the length of the alignment is the single most informative parameter. We demonstrate that some of the most popular programs in protein structure research differ considerably in their overall performance. In particular, each of the programs investigated here produced in at least in one case the best and the worst alignment compared with all others. Hence, at the current state of development of structure comparison techniques, it is advisable to use several programs in parallel and to choose the optimal alignment in the way reported here.

Availability and implementation: The computer software that implement the method described here is freely available at http://melolab.org/stovca.

Contact:  fmelo@bio.puc.cl
TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis
Authors: Lin Yu , Rajan Vaibhav , Moret Bernard M. E.
Published: October 2012

Summary: TIBA is a tool to reconstruct phylogenetic trees from rearrangement data that consist of ordered lists of synteny blocks (or genes), where each synteny block is shared with all of its homologues in the input genomes. The evolution of these synteny blocks, through rearrangement operations, is modelled by the uniform Double-Cut-and-Join model. Using a true distance estimate under this model and simple distance-based methods, TIBA reconstructs a phylogeny of the input genomes. Unlike any previous tool for inferring phylogenies from rearrangement data, TIBA uses novel methods of robustness estimation to provide support values for the edges in the inferred tree.

Availability:  http://lcbb.epfl.ch/softwares/tiba.html.

Contact:  vaibhav.rajan@epfl.ch
A high-performance computing toolset for relatedness and principal component analysis of SNP data
Authors: Zheng Xiuwen , Levine David , Shen Jess , Gogarten Stephanie M. , Laurie Cathy , Weir Bruce S.
Published: October 2012

Summary: Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed gdsfmt and SNPRelate (R packages for multi-core symmetric multiprocessing computer architectures) to accelerate two key computations on SNP data: principal component analysis (PCA) and relatedness analysis using identity-by-descent measures. The kernels of our algorithms are written in C/C++ and highly optimized. Benchmarks show the uniprocessor implementations of PCA and identity-by-descent are ∼8–50 times faster than the implementations provided in the popular EIGENSTRAT (v3.0) and PLINK (v1.07) programs, respectively, and can be sped up to 30–300-fold by using eight cores. SNPRelate can analyse tens of thousands of samples with millions of SNPs. For example, our package was used to perform PCA on 55 324 subjects from the ‘Gene-Environment Association Studies’ consortium studies.

Availability and implementation: gdsfmt and SNPRelate are available from R CRAN (http://cran.r-project.org), including a vignette. A tutorial can be found at https://www.genevastudy.org/Accomplishments/software.

Contact:  zhengx@u.washington.edu
GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies
Authors: Gogarten Stephanie M. , Bhangale Tushar , Conomos Matthew P. , Laurie Cecelia A. , McHugh Caitlin P. , Painter Ian , Zheng Xiuwen , Crosslin David R. , Levine David , Lumley Thomas , Nelson Sarah C. , Rice Kenneth , Shen Jess , Swarnkar Rohit , Weir Bruce S. , Laurie Cathy C.
Published: October 2012

Summary: GWASTools is an R/Bioconductor package for quality control and analysis of genome-wide association studies (GWAS). GWASTools brings the interactive capability and extensive statistical libraries of R to GWAS. Data are stored in NetCDF format to accommodate extremely large datasets that cannot fit within R’s memory limits. The documentation includes instructions for converting data from multiple formats, including variants called from sequencing. GWASTools provides a convenient interface for linking genotypes and intensity data with sample and single nucleotide polymorphism annotation.

Availability and implementation: GWASTools is implemented in R and is available from Bioconductor (http://www.bioconductor.org). An extensive vignette detailing a recommended work flow is included.

Contact:  sdmorris@uw.edu
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition
Authors: Sato Kengo , Kato Yuki , Akutsu Tatsuya , Asai Kiyoshi , Sakakibara Yasubumi
Published: October 2012

Motivation: It is well known that the accuracy of RNA secondary structure prediction from a single sequence is limited, and thus a comparative approach that predicts a common secondary structure from aligned sequences is a better choice if homologous sequences with reliable alignments are available. However, correct secondary structure information is needed to produce reliable alignments of RNA sequences. To tackle this dilemma, we require a fast and accurate aligner that takes structural information into consideration to yield reliable structural alignments, which are suitable for common secondary structure prediction.

Results: We develop DAFS, a novel algorithm that simultaneously aligns and folds RNA sequences based on maximizing expected accuracy of a predicted common secondary structure and its alignment. DAFS decomposes the pairwise structural alignment problem into two independent secondary structure prediction problems and one pairwise (non-structural) alignment problem by the dual decomposition technique, and maintains the consistency of a pairwise structural alignment by imposing penalties on inconsistent base pairs and alignment columns that are iteratively updated. Furthermore, we extend DAFS to consider pseudoknots in RNA structural alignments by integrating IPknot for predicting a pseudoknotted structure. The experiments on publicly available datasets showed that DAFS can produce reliable structural alignments from unaligned sequences in terms of accuracy of common secondary structure prediction.

Availability: The program of DAFS and the datasets are available at http://www.ncrna.org/software/dafs/.

Contact:  satoken@bio.keio.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Extensimonas vulgaris gen. nov., sp. nov., a member of the family

Comamonadaceae
Authors: Zhang Wei-Yan , Fang Ming-Xu , Zhang Wen-Wu , Xiao Chuan , Zhang Xin-Qi , Yu Zhi-Ping , Zhu Xu-Fen , Wu Min
Published: October 2012

A novel strain, named S4T, was obtained from industrial wastewater in Xiaoshan, Zhejiang Province, China. Cells were Gram-negative, neutrophilic and non-spore-forming and moved by means of a polar flagellum. Normal cells were 0.8–0.9×1.3–1.9 µm and the cells elongated to 10–25 µm when cultivated at high temperatures. Strain S4T grew at 15–50 °C (optimum at 48 °C), pH 5.5–8.5 (optimum 7.0–7.5) and 0–2 % (optimum 0.5 %) (w/v) NaCl. Ubiquinone-8 was the predominant respiratory quinone. C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C17 : 0 cyclo were the major cellular fatty acids. The major 3-OH fatty acid was C10 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminoglycolipid. The genomic DNA G+C content was 68.8 mol%. Based on 16S rRNA gene sequences alignment, the most closely related strains were members of the genera

Comamonas

(94.6–95.6 % similarities),

Giesbergeria

(94.9–95.6 %),

Acidovorax

(94.8–95.4 %),

Brachymonas

(94.1–95.2 %) and

Macromonas

(95.1 %). Phylogenetic analysis showed the closest relatives of strain S4T were members of the genus

Macromonas

. Based on phenotypic and phylogenetic characteristics, we suggest that strain S4T represents a novel species of a new genus of the family

Comamonadaceae

, for which the name Extensimonas vulgaris gen. nov., sp. nov. is proposed. The type strain of Extensimonas vulgaris is S4T ( = CGMCC 1.10977T = JCM 17803T).
Mariniradius saccharolyticus gen. nov., sp. nov., a member of the family

Cyclobacteriaceae

isolated from marine aquaculture pond water, and emended descriptions of the genus

Aquiflexum

and

Aquiflexum balticum
Authors: Bhumika V. , Srinivas T. N. R. , Ravinder K. , Anil Kumar P.
Published: October 2012

A novel marine, Gram-stain-negative, oxidase- and catalase- positive, rod-shaped bacterium, designated strain AK6T, was isolated from marine aquaculture pond water collected in Andhra Pradesh, India. The fatty acids were dominated by iso-C15 : 0, iso-C17 : 1ω9c, iso-C15 : 1 G, iso-C17 : 0 3-OH and anteiso-C15 : 0. Strain AK6T contained MK-7 as the sole respiratory quinone and phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid and seven unidentified lipids as polar lipids. The DNA G+C content of strain AK6T was 45.6 mol%. Phylogenetic analysis showed that strain AK6T formed a distinct branch within the family

Cyclobacteriaceae

and clustered with

Aquiflexum balticum

DSM 16537T and other members of the family

Cyclobacteriaceae

. 16S rRNA gene sequence analysis confirmed that

Aquiflexum balticum

DSM 16537T was the nearest neighbour, with pairwise sequence similarity of 90.1 %, while sequence similarity with the other members of the family was <88.5 %. Based on differentiating phenotypic characteristics and phylogenetic inference, strain AK6T is proposed as a representative of a new genus and species of the family

Cyclobacteriaceae

, as Mariniradius saccharolyticus gen. nov., sp. nov. The type strain of Mariniradius saccharolyticus is AK6T ( = MTCC 11279T = JCM 17389T). Emended descriptions of the genus

Aquiflexum

and

Aquiflexum balticum

are also proposed.
Flavobacterium noncentrifugens sp. nov., a psychrotolerant bacterium isolated from glacier meltwater
Authors: Zhu Lang , Liu Qing , Liu Hongcan , Zhang Jianli , Dong Xiuzhu , Zhou Yuguang , Xin Yuhua
Published: October 2012

A non-motile, Gram-stain-negative bacterium, designated R-HLS-17T, was isolated from the meltwater of Hailuogou Glacier located in Sichuan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus

Flavobacterium

, with the closest relatives being

Flavobacterium antarcticum

JCM 12383T (95.5 % 16S rRNA gene sequence similarity),

F. omnivorum

JCM 11313T (95.0 %) and

F. fryxellicola

LMG 22022T (95.2 %). Growth occurred at 0–29 °C (optimum, 10–20 °C) and pH 6.0–8.5 (optimum, 7.0–8.0). The DNA G+C content was 46.5 mol%. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0), iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The predominant menaquinone was MK-6. Based on the genotypic and phenotypic characteristics, we propose that strain R-HLS-17T represents a novel species of the genus

Flavobacterium

, Flavobacterium noncentrifugens sp. nov. The type strain is R-HLS-17T ( = CGMCC 1.10076T = NBRC 108844T).
Characterization of a serine-to-asparagine substitution at position 123 in the Japanese encephalitis virus E protein
Authors: Yamaguchi Yukie , Nukui Yoko , Kotaki Akira , Sawabe Kyoko , Saijo Masayuki , Watanabe Haruo , Kurane Ichiro , Takasaki Tomohiko , Tajima Shigeru
Published: October 2012

Amino acid position 123 in the E protein of Japanese encephalitis virus (JEV) determines viral growth properties and pathogenicity. The majority of JEV strains have a serine residue at this position (E123S); however, JEV with an asparagine residue (E123N) has also been isolated. To compare the growth properties and pathogenicity of E123Sand E123NJEV, we produced recombinant JEV with a serine-to-asparagine substitution at position 123 (rJEV-Mie41-ES123N) in the E123S-type strain Mie/41/2002 background. The growth rate of rJEV-Mie41-ES123Nwas similar to that of Mie/41/2002 in mammalian and mosquito cell lines. Mouse challenge experiments showed that there was only a slight difference in neuroinvasiveness between the parent strain (Mie/41/2002) and rJEV-Mie41-ES123N. Thus, our results indicate that the Ser-to-Asn substitution in the JEV E protein has weak impact on viral growth propertiesin vitroor on pathogenicityin vivo.
The human cathelicidin LL-37 inhibits influenza A viruses through a mechanism distinct from that of surfactant protein D or defensins
Authors: Tripathi Shweta , Tecle Tesfaldet , Verma Anamika , Crouch Erika , White Mitchell , Hartshorn Kevan L.
Published: October 2012

LL-37, the only human cathelicidin, is a cationic antimicrobial peptide with antibacterial and antifungal activity. LL-37 is released from neutrophil granules and produced by epithelial cells. It has been implicated in host defence against influenza A virus (IAV) in recent studies. We now demonstrate dose-related neutralizing activity of LL-37 against several seasonal and mouse-adapted IAV strains. The ability of LL-37 to inhibit these IAV strains resulted mainly from direct effects on the virus, since pre-incubation of virus with LL-37 was needed for optimal inhibition. LL-37 bound high-density lipoprotein (HDL), and pre-incubation of LL-37 with human serum or HDL reduced its antiviral activity. LL-37 did not inhibit viral association with epithelial cells as assessed by quantitative RT-PCR or confocal microscopy. This finding contrasted with results obtained with surfactant protein D (SP-D). Unlike collectins or human neutrophil defensins (HNPs), LL-37 did not induce viral aggregation under electron microscopy. In the electron microscopy studies, LL-37 appeared to cause disruption of viral membranes. LL-37 had additive antiviral activity when combined with other innate inhibitors like SP-D, surfactant protein A and HNPs. Unlike HNPs, LL-37 did not bind SP-D significantly. These findings indicate that LL-37 contributes to host defence against IAV through a mechanism distinct from that of SP-D and HNPs.
Deletion of the C-terminal ESEV domain of NS1 does not affect the replication of a low-pathogenic avian influenza virus H7N1 in ducks and chickens
Authors: Soubies Sébastien M. , Hoffmann Thomas W. , Croville Guillaume , Larcher Thibaut , Ledevin Mireille , Soubieux Denis , Quéré Pascale , Guérin Jean-Luc , Marc Daniel , Volmer Romain
Published: October 2012

Highly pathogenic avian influenza (HPAI) H7N1 viruses caused a series of epizootics in Italy between 1999 and 2001. The emergence of these HPAI viruses coincided with the deletion of the six amino acids R225VESEV230at the C terminus of NS1. In order to assess how the truncation of NS1 affected virus replication, we used reverse genetics to generate a wild-type low-pathogenic avian influenza (LPAI) H7N1 virus with a 230aa NS1 (H7N1230) and a mutant virus with a truncated NS1 (H7N1224). The 6aa truncation had no impact on virus replication in duck or chicken cellsin vitro. The H7N1230and H7N1224viruses also replicated to similar levels and induced similar immune responses in ducks or chickens. No significant histological lesions were detected in infected ducks, regardless of the virus inoculated. However, in chickens, the H7N1230virus induced a more severe interstitial pneumonia than did the H7N1224virus. These findings indicate that the C-terminal extremity of NS1, including the PDZ-binding motif ESEV, is dispensable for efficient replication of an LPAI virus in ducks and chickens, even though it may increase virulence in chickens, as revealed by the intensity of the histological lesions.
Dynamic localization of two tobamovirus ORF6 proteins involves distinct organellar compartments
Authors: Gushchin Vladimir A. , Lukhovitskaya Nina I. , Andreev Dmitri E. , Wright Kathryn M. , Taliansky Michael E. , Solovyev Andrey G. , Morozov Sergey Y. , MacFarlane Stuart A.
Published: October 2012

ORF6 is a small gene that overlaps the movement and coat protein genes of subgroup 1a tobamoviruses. The ORF6 protein of tomato mosaic virus (ToMV) strain L (L-ORF6), interacts in vitro with eukaryotic elongation factor 1α, and mutation of the ORF6 gene of tobacco mosaic virus (TMV) strain U1 (U1-ORF6) reduces the pathogenicity in vivo of TMV, whereas expression of this gene from two other viruses, tobacco rattle virus (TRV) and potato virus X (PVX), increases their pathogenicity. In this work, the in vivo properties of the L-ORF6 and U1-ORF6 proteins were compared to identify sequences that direct the proteins to different subcellular locations and also influence virus pathogenicity. Site-specific mutations in the ORF6 protein were made, hybrid ORF6 proteins were created in which the N-terminal and C-terminal parts were derived from the two proteins, and different subregions of the protein were examined, using expression either from a recombinant TRV vector or as a yellow fluorescent protein fusion from a binary plasmid in Agrobacterium tumefaciens. L-ORF6 caused mild necrotic symptoms in Nicotiana benthamiana when expressed from TRV, whereas U1-ORF6 caused severe symptoms including death of the plant apex. The difference in symptoms was associated with the C-terminal region of L-ORF6, which directed the protein to the endoplasmic reticulum (ER), whereas U1-ORF6 was directed initially to the nucleolus and later to the mitochondria. Positively charged residues at the N terminus allowed nucleolar entry of both U1-ORF6 and L-ORF6, but hydrophobic residues at the C terminus of L-ORF6 directed this protein to the ER.
Vesicular stomatitis virus as a flexible platform for oncolytic virotherapy against cancer
Authors: Hastie Eric , Grdzelishvili Valery Z.
Published: October 2012

Oncolytic virus (OV) therapy is an emerging anti-cancer approach that utilizes viruses to preferentially infect and kill cancer cells, while not harming healthy cells. Vesicular stomatitis virus (VSV) is a prototypic non-segmented, negative-strand RNA virus with inherent OV qualities. Antiviral responses induced by type I interferon pathways are believed to be impaired in most cancer cells, making them more susceptible to VSV than normal cells. Several other factors make VSV a promising OV candidate for clinical use, including its well-studied biology, a small, easily manipulated genome, relative independence of a receptor or cell cycle, cytoplasmic replication without risk of host-cell transformation, and lack of pre-existing immunity in humans. Moreover, various VSV-based recombinant viruses have been engineered via reverse genetics to improve oncoselectivity, safety, oncotoxicity and stimulation of tumour-specific immunity. Alternative delivery methods are also being studied to minimize premature immune clearance of VSV. OV treatment as a monotherapy is being explored, although many studies have employed VSV in combination with radiotherapy, chemotherapy or other OVs. Preclinical studies with various cancers have demonstrated that VSV is a promising OV; as a result, a human clinical trial using VSV is currently in progress.
Whole-genome analysis of two bovine rotavirus C strains: Shintoku and Toyama
Authors: Soma Junichi , Tsunemitsu Hiroshi , Miyamoto Takeshi , Suzuki Goro , Sasaki Takashi , Suzuki Tohru
Published: October 2012

Rotavirus C (RVC) has been detected frequently in epidemic cases and/or outbreaks of diarrhoea in humans and animals worldwide. Because it is difficult to cultivate RVCs serially in cell culture, the sequence data available for RVCs are limited, despite their potential economical and epidemiological impact. Although whole-genome sequences of one porcine RVC and seven human RVC strains have been analysed, this has not yet been done for a bovine RVC strain. In the present study, we first determined the nucleotide sequences for five as-yet underresearched genes, including the NSP4 gene, from a cultivable bovine RVC, the Shintoku strain, identified in Hokkaido Prefecture, Japan, in 1991. In addition, we elucidated the ORF sequences of all segments from another bovine RVC, the Toyama strain, detected in Toyama Prefecture, Japan, in 2010, in order to investigate genetic divergence among bovine RVCs. Comparison of segmental nucleotide and deduced amino acid sequences among RVCs indicates high identity among bovine RVCs and low identity between human and porcine RVCs. Phylogenetic analysis of each gene showed that the two bovine RVCs belong to a cluster distinct from human and porcine RVCs. These data demonstrate that RVCs can be classified into different genotypes according to host species. Moreover, RVC NSP1, NSP2 and VP1 amino acid sequences contain a unique motif that is highly conserved among rotavirus A (RVA) strains and, hence, several proteins from bovine RVCs are suggested to play important roles that are similar to those of RVAs.
Identification of an avian group A rotavirus containing a novel VP4 gene with a close relationship to those of mammalian rotaviruses
Authors: Trojnar Eva , Sachsenröder Jana , Twardziok Sven , Reetz Jochen , Otto Peter H. , Johne Reimar
Published: October 2012

Group A rotaviruses (RVAs) are an important cause of diarrhoeal illness in humans, as well as in mammalian and avian animal species. Previous sequence analyses indicated that avian RVAs are related only distantly to mammalian RVAs. Here, the complete genomes of RVA strain 03V0002E10 from turkey (Meleagris gallopavo) and RVA strain 10V0112H5 from pheasant (Phasianus colchicus) were analysed using a combination of 454 deep sequencing and Sanger sequencing technologies. An adenine-rich insertion similar to that found in the chicken RVA strain 02V0002G3, but considerably shorter, was found in the 3′ NCR of the NSP1 gene of the pheasant strain. Most genome segments of both strains were related closely to those of avian RVAs. The novel genotype N10 was assigned to the NSP2 gene of the pheasant RVA, which is related most closely to genotype N6 found in avian RVAs. However, this virus contains a VP4 gene of the novel genotype P[37], which is related most closely to RVAs from pigs, dogs and humans. This strain either may represent an avian/mammalian rotavirus reassortant, or it carries an unusual avian rotavirus VP4 gene, thereby broadening the potential genetic and antigenic variability among RVAs.
An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence
Authors: Liu Yiwei , Toh Hidehiro , Sasaki Hiroyuki , Zhang Xing , Cheng Xiaodong
Published: October 2012

Zinc finger transcription factor Zfp57 recognizes the methylated CpG within the TGCCGC element. We determined the structure of the DNA-binding domain of Zfp57, consisting of two adjacent zinc fingers, in complex with fully methylated DNA at 1.0 Å resolution. The first zinc finger contacts the 5′ half (TGC), and the second recognizes the 3′ half (CGC) of the recognition sequence. Zfp57 recognizes the two 5-methylcytosines (5mCs) asymmetrically: One involves hydrophobic interactions with Arg178, which also interacts with the neighboring 3′ guanine and forms a 5mC–Arg-G interaction, while the other involves a layer of ordered water molecules. Two point mutations in patients with transient neonatal diabetes abolish DNA-binding activity. Zfp57 has reduced binding affinity for unmodified DNA and the oxidative products of 5mC.
A new crystal form of MshB fromMycobacterium tuberculosiswith glycerol and acetate in the active site suggests the catalytic mechanism
Authors: Broadley Simon Gareth , Gumbart James Conrad , Weber Brandon William , Marakalala Mohlopheni Jackson , Steenkamp Daniel Jacobus , Sewell Bryan Trevor
Published: October 2012

MshB, a zinc-based deacetylase, catalyses a step in the mycothiol biosynthetic pathway that involves the deacetylation of 1-O-(2-acetamido-2-deoxy-α-D-glucopyranosyl)-D-myo-inositol (GlcNAc-Ins),viacleavage of an amide bond, to 1-O-(2-amino-2-deoxy-α-D-glucopyranosyl)-D-myo-inositol (GlcN-Ins) and acetate. In this study, MshB was expressed, purified and crystallized. A new crystal form was encountered in 0.1 Msodium acetate, 0.2 Mammonium sulfate, 25% PEG 4000 pH 4.6. The crystals diffracted to 1.95 Å resolution and the resulting electron-density map revealed glycerol and the reaction product, acetate, in the active site. These ligands enabled the natural substrate GlcNAc-Ins to be modelled in the active site with some certainty. One acetate O atom is hydrogen bonded to Tyr142 and is located 2.5 Å from the catalytic zinc. The other acetate O atom is located 2.7 Å from a carboxylate O atom of Asp15. This configuration strongly suggests that Asp15 acts both as a general base catalyst in the nucleophilic attack of water on the amide carbonyl C atom and in its protonated form acts as a general acid to protonate the amide N atom. The configuration of Tyr142 differs from that observed previously in crystal structures of MshB (PDB entries 1q74 and 1q7t) and its location provides direct structural support for recently published biochemical and mutational studies suggesting that this residue is involved in a conformational change on substrate binding and contributes to the oxyanion hole that stabilizes the tetrahedral intermediate.
Clinical comparison of the pneumatic and the combined lithotripters in percutaneous nephrolithotomy
Authors: Koc Gokhan , Akbay Kaan Esat , Tarhan Huseyin , Cakmak Ozgur , Yilmaz Yuksel
Published: October 2012

Aim

To compare the effectiveness of the pneumatic lithotripter and the combined lithotripter (pneumatic + ultrasonic) in percutaneous nephrolithotomy (PNL).

Patients and Methods

A total of 150 patients who underwent PNL between March 2009 and January 2011 were included in the study. In the first 49 cases, only the pneumatic lithotripter (group 1) was used, while in the next 101 patients, combined lithotripter (group 2) was used. Differences with regard to total clearance time, fluoroscopic screening time (FST), duration of hospital stay, duration of nephrostomy removal, haematocrit loss, blood transfusion rate and successful treatment rate were investigated between the two groups.

Results

The general characteristics of the patients were similar between the two groups. However, the mean stone size was statistically significantly higher in group 2. No statistically‐significant difference was detected between the two groups in terms of hospital stay, nephrostomy removal days, successful treatment rate and blood transfusion rate, but compared to group 1 patients, total clearance time, FST and haematocrit loss were significantly less in group 2.

Conclusion

Although pneumatic and ultrasonic lithotripters are both sufficiently effective when used separately, the combined device was observed to positively influence total clearance time, FST and haematocrit loss significantly.
Assessment of block height for satisfactory spinal anaesthesia for caesarean section
Authors: Ousley R. , Egan C. , Dowling K. , Cyna A. M.
Published: October 2012

We investigated block heights that anaesthetists considered adequate for caesarean section to proceed under spinal anaesthesia. During 3 months, 15 obstetric anaesthetists recorded block height to touch, pinprick or cold when spinal anaesthesia was considered satisfactory for caesarean section to proceed. Median (IQR [range]) block height for touch, pinprick, first cold and icy were: T10 (T7–T12 [T3–L1]); T5 (T4–T6 [C7–L1]); T5 (T4–T6 [C7–L1]); and T3 (T2–T4 [C7–L1]), respectively. Modalities were significantly correlated for: touch and cold, p = 0.0001; touch and icy, p = 0.0007; touch and pinprick, p = 0.0018; cold and icy, p < 0.0001; cold and pinprick, p = 0.0001; icy and pinprick, p < 0.0001. Pairwise comparisons showed differences between all modalities (p < 0.001) apart from pinprick and first cold (p = 0.94). All women had satisfactory anaesthesia despite 76 (81%) having a block to touch below T6. Single modality assessment of block height, particularly using touch, may erroneously indicate inadequate anaesthesia for caesarean section.
Modified patient‐controlled remifentanil bolus delivery regimen for labour pain*
Authors: Jost A. , Ban B. , Kamenik M.
Published: October 2012

To improve the analgesic efficiency and to simplify the administration of remifentanil for systemic analgesia in labour, we contrived a modified delivery regimen with a specific infusion profile and variable dosing and conducted a single‐blind randomised crossover study to compare it with the previous ‘classical’ regimen. Parturients received both regimens in interchangeable sets, each with five contractions. We compared pain and satisfaction scores, maternal and fetal vital parameters, side‐effects and other events. Twenty‐three parturients completed the study. No differences in observed parameters were noticed except for slightly lower blood pressure with the modified regimen. Pain estimates were lower in women starting with the modified regimen (p = 0.005), and there were fewer requests for analgesia within the lockout period (31 vs 69, p = 0.041) and bolus adjustments (0 vs 25, p < 0.001) with the modified regimen.
Thromboelastography to monitor the intra‐operative effects of low‐molecular weight heparin following bridging anticoagulation in a child with normal renal function*
Authors: Casey M. E. , Hodges O. , Dunn R. , Thomas J.
Published: October 2012

Paediatric patients who require anticoagulation with therapeutic doses of low‐molecular weight heparin are at risk of having a residual anticoagulant effect at the time of surgery, even if managed according to current peri‐operative guidelines. Testing for residual effect is not currently recommended in such circumstances. A 15‐year‐old child with a mechanical aortic valve replacement requiring long‐term warfarin treatment, as well as underlying coagulation defects, was administered low‐molecular weight heparin for bridging anticoagulation before kyphoscoliosis surgery. Thromboelastography was used intra‐operatively to diagnose residual heparinisation, which was demonstrated by a prolonged reaction (R) time of 16.0 min in the plain cup, compared with 9.2 min in the heparinase cup. Subsequently, thromboelastography was also used to monitor haemostatic therapy, which consisted of protamine 2 mg.kg−1 and 500 IU cryoprecipitate. Thromboelastography was used intra‐operatively to allow rapid testing of coagulation status and guide therapy, thereby minimising use of blood products and reducing complications.
The effect of warm ischemia at uterus transplantation in a rat model
Authors: DÍAZ‐GARCÍA CÉSAR , AKHI SHAMIMA N. , MARTÍNEZ‐VAREA ALICIA , BRÄNNSTRÖM MATS
Published: October 2012

Objective. Uterus transplantation (UTx) has been proposed as a method to treat women with absolute uterine factor infertility. The aim of this study was to evaluate the viability of the transplanted rat uterus after exposure to long warm ischemic times, in order to mimic a time frame likely to occur in a human situation during complicated pelvic vascular anastomosis surgery. Design. Experimental study. Setting. Obstetrics and Gynecology Department. Population. Female Lewis rats. Methods. Pseudopregnant rats were randomly allocated into two intervention groups, a standardized syngeneic UTx procedure (control; n = 10) and a modified UTx protocol with a four hour extended period of warm ischemia (n = 10). Main outcome measures. Scoring systems of gross morphology and histology at three and six days after transplantation. Results. Evident signs of necrosis were seen in five of 10 animals in the warm ischemia group compared with only one of 10 in the control group. Overall, uterine grafts from the warm ischemia group obtained poorer gross morphology scores. Histological findings correlated with the surgical findings at inspections three and six days after surgery. Conclusions. An extended warm ischemic time has detrimental effects on the survival of the uterus after transplantation.
Maternal inflammatory response to microbial invasion of the amniotic cavity: analyses of multiple proteins in the maternal serum
Authors: COBO TERESA , TSIARTAS PANAGIOTIS , KACEROVSKY MARIAN , HOLST ROSE‐MARIE , HOUGAARD DAVID M. , SKOGSTRAND KRISTIN , WENNERHOLM ULLA‐BRITT , HAGBERG HENRIK , JACOBSSON BO
Published: October 2012

Objective. To evaluate the maternal inflammatory response to microbial invasion of the amniotic cavity (MIAC) in women with preterm labor and preterm prelabor rupture of membranes using selected proteins in the maternal serum. Design. A prospective cohort study. Setting. Labor ward from Salgrenska University Hospital. The evaluation of the maternal inflammatory response in the presence of MIAC in preterm labor and preterm prelabor rupture of membranes. Population. One hundred and sixteen women with preterm labor and 73 women with preterm prelabor rupture of membranes between the gestational ages of 22+0 and 33+6 weeks. Methods. Twenty‐seven maternal serum proteins were assayed by a multiple immunoassay. Main outcome measures. The maternal serum inflammatory response was evaluated according to the presence of MIAC. Data were stratified by gestational age. Results. There were few differences in the maternal serum protein levels when MIAC was present in both preterm labor and preterm prelabor rupture of membranes. In preterm prelabor rupture of membranes, higher levels of interleukin‐18 (median 654 vs. 361 pg/mL, p= 0.003) and lower levels of interleukin‐1β (9.5 vs. 19.9 pg/mL, p= 0.008) and monocyte chemotactic protein‐1 (139.1 vs. 212.6 pg/mL, p= 0.039) were observed in women with MIAC. Interleukin‐6 (20.8 vs. 13.9 pg/mL, p= 0.019) was the only biomarker that increased significantly in preterm labor complicated with MIAC. All of the differences between preterm labor and preterm prelabor rupture of membranes were observed at less than 32+0 weeks of gestation. Conclusions. A weak maternal inflammatory response in the serum was observed in women with MIAC.
Expressed breast milk for procedural pain in preterm neonates: a randomized, double‐blind, placebo‐controlled trial
Authors: Ou‐Yang Mei‐Chen , Chen I‐Lun , Chen Chih‐Cheng , Chung Mei‐Yung , Chen Feng‐Shun , Huang Hsin‐Chun
Published: October 2012

Aim

To determine whether expressed breast milk (milk) reduces procedural pain associated with heel lancing in preterm neonates.

Methods

In this placebo‐controlled trial, preterm neonates received 5 mL of distilled water as placebo (water, n = 44), 25% glucose water (glucose, n = 39) or milk (n = 40). Heel lancing was performed 2 min later. The primary outcome was the duration of first cry after lancing.

Results

Participants had similar baseline demographic and clinical characteristics. There was a significant difference in the median duration of first cry among the groups: water = 70.5 sec [interquartile range (IQR) = 5.5–104.5]; glucose = 2.0 sec (IQR = 0.0–45.0); milk = 29.5 sec (IQR = 0.0–65.0). Specifically, the duration of first cry was significantly shorter in the glucose group compared with the water group (Bonferroni adjustment, p = 0.011). Pain scores were significantly lower in the glucose and milk groups compared with the water group 1, 2 and 3 min after heel lancing (p < 0.05).

Conclusions

Although milk did not significantly reduce crying time, our finding that pain scores were significantly lower in the milk group suggests that milk may reduce pain associated with heel lancing in preterm neonates.
Sustained unemployment in psychiatric outpatients with bipolar depression compared to major depressive disorder with comorbid borderline personality disorder
Authors: Zimmerman Mark , Martinez Jennifer H , Young Diane , Chelminski Iwona , Dalrymple Kristy
Published: October 2012

Zimmerman M, Martinez JH, Young D, Chelminski I, Dalrymple K. Sustained unemployment in psychiatric outpatients with bipolar depression compared to major depressive disorder with comorbid borderline personality disorder. Bipolar Disord 2012: 14: 856–862. © 2012 John Wiley & Sons A/S.Published by Blackwell Publishing Ltd.

Objectives:  The morbidity associated with bipolar disorder is, in part, responsible for repeated calls for improved detection and recognition. No such clinical commentary exists for improved detection of borderline personality disorder in depressed patients. Clinical experience suggests that borderline personality disorder is as disabling as bipolar disorder; however, no studies have directly compared the two disorders. For this reason we undertook the current analysis from the Rhode Island Methods to Improve Diagnostic Assessment and Services (MIDAS) project comparing unemployment and disability rates in patients with bipolar disorder and borderline personality disorder.

Methods:  Patients were interviewed with semi‐structured interviews. We compared three non‐overlapping groups of depressed patients: (i) 181 patients with DSM–IV major depressive disorder and borderline personality disorder, (ii) 1068 patients with major depressive disorder without borderline personality disorder, and (iii) 84 patients with bipolar depression without borderline personality disorder.

Results:  Compared to depressed patients without borderline personality disorder, depressed patients with borderline personality disorder were significantly more likely to have been persistently unemployed. A similar difference was found between patients with bipolar depression and major depressive disorder without borderline personality disorder. No differences were found between patients with bipolar depression and depression with borderline personality disorder.

Conclusions:  Both bipolar disorder and borderline personality disorder were associated with impaired occupational functioning and thus carry a significant public health burden. Efforts to improve detection of borderline personality disorder in depressed patients might be as important as the recognition of bipolar disorder.
Noradrenaline stimulates cell proliferation by suppressing potassium channels via Gi/o‐protein‐coupled α1B‐adrenoceptors in human osteoblasts
Authors: Kodama D , Togari A
Published: October 2012

Background and Purpose

Recent studies demonstrated that the sympathetic nervous system regulates bone metabolism via β2‐adrenoceptors. Although α‐adrenoceptors are also expressed in osteogenic cells, their functions in bone metabolism have been less studied. We previously demonstrated that noradrenaline suppressed potassium currents via α1B‐adrenoceptors in the human osteoblast SaM‐1 cell line. The aim of this study was to investigate the signal transduction pathway and the physiological role of noradrenaline in human osteoblasts in more detail.

Experimental Approach

To investigate signal transduction through α1B‐adrenoceptors, we used whole‐cell patch clamp recording and Ca fluorescence imaging. Potassium channels regulate membrane potential and cell proliferation activity in non‐excitable cells, so we evaluated cell proliferation activity by BrdU incorporation and WST assay.

Key Results

In SaM‐1 cells, bath‐applied noradrenaline elevated intracellular Ca2+ concentration and this effect was abolished by both chloroethylclonidine, an α1B‐adrenoceptor antagonist, and U73122, a PLC inhibitor. However, the inhibitory effect of noradrenaline on whole‐cell current was unaffected by U73122. In contrast, in cells pretreated with either Pertussis toxin, a Gi/o‐protein‐coupled receptor inhibitor, or gallein, a Gβγ‐protein inhibitor, the inhibitory effect of noradrenaline on whole‐cell current was significantly suppressed. Noradrenaline‐induced enhancement of cell proliferation was inhibited by CsCl, a non‐selective potassium channel blocker, gallein and H89, a PKA inhibitor, but not by U73122.

Conclusions and Implications

Noradrenaline facilitated cell proliferation by regulation of potassium currents in human osteoblasts via Gi/o‐protein‐coupled α1B‐adrenoceptors, not via coupling to Gq‐proteins.
Mechanisms of zolpidem‐induced long QT syndrome: acute inhibition of recombinant hERG K+ channels and action potential prolongation in human cardiomyocytes derived from induced pluripotent stem cells
Authors: Jehle J , Ficker E , Wan X , Deschenes I , Kisselbach J , Wiedmann F , Staudacher I , Schmidt C , Schweizer PA , Becker R , Katus HA , Thomas D
Published: October 2012

Background and Purpose

Zolpidem, a short‐acting hypnotic drug prescribed to treat insomnia, has been clinically associated with acquired long QT syndrome (LQTS) and torsade de pointes (TdP) tachyarrhythmia. LQTS is primarily attributed to reduction of cardiac human ether‐a‐go‐go‐related gene (hERG)/IKr currents. We hypothesized that zolpidem prolongs the cardiac action potential through inhibition of hERG K+ channels.

Experimental Approach

Two‐electrode voltage clamp and whole‐cell patch clamp electrophysiology was used to record hERG currents from Xenopus oocytes and from HEK 293 cells. In addition, hERG protein trafficking was evaluated in HEK 293 cells by Western blot analysis, and action potential duration (APD) was assessed in human‐induced pluripotent stem cell (hiPSC)‐derived cardiomyocytes.

Key Results

Zolpidem caused acute hERG channel blockade in oocytes (IC50 = 61.5 μM) and in HEK 293 cells (IC50 = 65.5 μM). Mutation of residues Y652 and F656 attenuated hERG inhibition, suggesting drug binding to a receptor site inside the channel pore. Channels were blocked in open and inactivated states in a voltage‐ and frequency‐independent manner. Zolpidem accelerated hERG channel inactivation but did not affect I–V relationships of steady‐state activation and inactivation. In contrast to the majority of hERG inhibitors, hERG cell surface trafficking was not impaired by zolpidem. Finally, acute zolpidem exposure resulted in APD prolongation in hiPSC‐derived cardiomyocytes.

Conclusions and Implications

Zolpidem inhibits cardiac hERG K+ channels. Despite a relatively low affinity of zolpidem to hERG channels, APD prolongation may lead to acquired LQTS and TdP in cases of reduced repolarization reserve or zolpidem overdose.
Agonists with supraphysiological efficacy at the muscarinic M2 ACh receptor
Authors: Schrage R , Seemann WK , Klöckner J , Dallanoce C , Racké K , Kostenis E , De Amici M , Holzgrabe U , Mohr K
Published: October 2012

Background and Purpose

Artificial agonists may have higher efficacy for receptor activation than the physiological agonist. Until now, such ‘superagonism’ has rarely been reported for GPCRs. Iperoxo is an extremely potent muscarinic receptor agonist. We hypothesized that iperoxo is a ‘superagonist’.

Experimental Approach

Signalling of iperoxo and newly synthesized structural analogues was compared with that of ACh at label‐free M2 muscarinic receptors applying whole cell dynamic mass redistribution, measurement of G‐protein activation, evaluation of cell surface agonist binding and computation of operational efficacies.

Key Results

In CHO‐hM2 cells, iperoxo significantly exceeds ACh in Gi/Gs signalling competence. In the orthosteric loss‐of‐function mutant M2‐Y1043.33A, the maximum effect of iperoxo is hardly compromised in contrast to ACh. ‘Superagonism’ is preserved in the physiological cellular context of MRC‐5 human lung fibroblasts. Structure–signalling relationships including iperoxo derivatives with either modified positively charged head group or altered tail suggest that ‘superagonism’ of iperoxo is mechanistically based on parallel activation of the receptor protein via two orthosteric interaction points.

Conclusion and Implications

Supraphysiological agonist efficacy at muscarinic M2 ACh receptors is demonstrated for the first time. In addition, a possible underlying molecular mechanism of GPCR ‘superagonism’ is provided. We suggest that iperoxo‐like orthosteric GPCR activation is a new avenue towards a novel class of receptor activators.

Linked Article

This article is commented on by Langmead and Christopoulos, pp. 353–356 of this issue. To view this commentary visit http://dx.doi.org/10.1111/bph.12142
The anti‐cancer agent SU4312 unexpectedly protects against MPP+‐induced neurotoxicity via selective and direct inhibition of neuronal NOS
Authors: Cui Wei , Zhang Zaijun , Li Wenming , Hu Shengquan , Mak Shinghung , Zhang Huan , Han Renwen , Yuan Shuai , Li Sai , Sa Fei , Xu Daping , Lin Zhixiu , Zuo Zhong , Rong Jianhui , Ma Edmond Dik‐Lung , Choi Tony Chunglit , Lee Simon MY , Han Yifan
Published: October 2012

Background and Purpose

SU4312, a potent and selective inhibitor of VEGF receptor‐2 (VEGFR‐2), has been designed to treat cancer. Recent studies have suggested that SU4312 can also be useful in treating neurodegenerative disorders. In this study, we assessed neuroprotection by SU4312 against 1‐methyl‐4‐phenylpyridinium ion (MPP+)‐induced neurotoxicity and further explored the underlying mechanisms.

Experimental Approach

MPP+‐treated neurons and 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP)‐treated zebrafish were used to study neuroprotection by SU4312. NOS activity was assayed in vitro to examine direct interactions between SU4312 and NOS isoforms.

Key Results

SU4312 unexpectedly prevented MPP+‐induced neuronal apoptosis in vitro and decreased MPTP‐induced loss of dopaminergic neurons, reduced expression of mRNA for tyrosine hydroxylase and impaired swimming behaviour in zebrafish. In contrast, PTK787/ZK222584, a well‐studied VEGFR‐2 inhibitor, failed to prevent neurotoxicity, suggesting that the neuroprotective actions of SU4312 were independent of its anti‐angiogenic action. Furthermore, SU4312 exhibited non‐competitive inhibition of purified neuronal NOS (nNOS) with an IC50 value of 19.0 μM but showed little or no effects on inducible and endothelial NOS. Molecular docking simulations suggested an interaction between SU4312 and the haem group within the active centre of nNOS.

Conclusions and Implication

SU4312 exhibited neuroprotection against MPP+ at least partly via selective and direct inhibition of nNOS. Because SU4312 could reach the brain in rats, our study also offered a support for further development of SU4312 to treat neurodegenerative disorders, particularly those associated with NO‐mediated neurotoxicity.