bluuebunny/crossref_metadata_2025 huggingface dataset:
Creating views on integrated multidomain data
Authors: Rohn Hendrik , Klukas Christian , Schreiber Falk
Published: May 2011

Motivation: Modern data acquisition methods in biology allow the procurement of different types of data in increasing quantity, facilitating a comprehensive view of biological systems. As data are usually gathered and interpreted by separate domain scientists, it is hard to grasp multidomain properties and structures. Consequently, there is a need for the integration of biological data from different sources and of different types in one application, providing various visualization approaches.

Results: In this article, methods for the integration and visualization of multimodal biological data are presented. This is achieved based on two graphs representing the meta-relations between biological data and the measurement combinations, respectively. Both graphs are linked and serve as different views of the integrated data with navigation and exploration possibilities. Data can be combined and visualized multifariously, resulting in views of the integrated biological data.

Availability:  http://vanted.ipk-gatersleben.de/hive/.

Contact:  rohn@ipk-gatersleben.de
Integrative gene network construction for predicting a set of complementary prostate cancer genes
Authors: Ahn Jaegyoon , Yoon Youngmi , Park Chihyun , Shin Eunji , Park Sanghyun
Published: May 2011

Motivation: Diagnosis and prognosis of cancer and understanding oncogenesis within the context of biological pathways is one of the most important research areas in bioinformatics. Recently, there have been several attempts to integrate interactome and transcriptome data to identify subnetworks that provide limited interpretations of known and candidate cancer genes, as well as increase classification accuracy. However, these studies provide little information about the detailed roles of identified cancer genes.

Results: To provide more information to the network, we constructed the network by incorporating genetic interactions and manually curated gene regulations to the protein interaction network. To make our newly constructed network cancer specific, we identified edges where two genes show different expression patterns between cancer and normal phenotypes. We showed that the integration of various datasets increased classification accuracy, which suggests that our network is more complete than a network based solely on protein interactions. We also showed that our network contains significantly more known cancer-related genes than other feature selection algorithms. Through observations of some examples of cancer-specific subnetworks, we were able to predict more detailed and interpretable roles of oncogenes and other cancer candidate genes in the prostate cancer cells.

Availability:  http://embio.yonsei.ac.kr/~Ahn/tc.php.

Contact:  sanghyun@cs.yonsei.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing
Authors: Walenz Brian , Florea Liliana
Published: May 2011

Summary: The large number of genomes that will be sequenced will need to be annotated with genes and other functional features. Aligning gene sequences from a related species to the target genome is an economical and highly reliable method to identify genes; unfortunately, existing tools have been lacking in sensitivity and speed. A program we reported, sim4cc, was shown to be highly accurate but is limited to comparing one cDNA with one genomic sequence. We present here an optimization of the tool, implemented in the packages sim4db and leaff. The new tool performs batch alignments of cDNA and genomic sequences in a fraction of the time required by its predecessor, and thus is very well suited for genome-wide analyses.

Availability:  Sim4db and leaff are written in C, C++ and Perl for Linux and other Unix platforms. Source code is distributed free of charge from http://sourceforge.net/projects/kmer/.

Contact:  florea@umiacs.umd.edu

Supplementary information:  Supplementary data are available at Bioinformatics Online.
An MCMC algorithm for detecting short adjacent repeats shared by multiple sequences
Authors: Li Qiwei , Fan Xiaodan , Liang Tong , Li Shuo−Yen R.
Published: May 2011

Motivation: Repeats detection problems are traditionally formulated as string matching or signal processing problems. They cannot readily handle gaps between repeat units and are incapable of detecting repeat patterns shared by multiple sequences. This study detects short adjacent repeats with interunit insertions from multiple sequences. For biological sequences, such studies can shed light on molecular structure, biological function and evolution.

Results: The task of detecting short adjacent repeats is formulated as a statistical inference problem by using a probabilistic generative model. An Markov chain Monte Carlo algorithm is proposed to infer the parameters in a de novo fashion. Its applications on synthetic and real biological data show that the new method not only has a competitive edge over existing methods, but also can provide a way to study the structure and the evolution of repeat-containing genes.

Availability: The related C++ source code and datasets are available at http://ihome.cuhk.edu.hk/%7Eb118998/share/BASARD.zip.

Contact:  xfan@sta.cuhk.edu.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
The role of indirect connections in gene networks in predicting function
Authors: Gillis Jesse , Pavlidis Paul
Published: May 2011

Motivation: Gene networks have been used widely in gene function prediction algorithms, many based on complex extensions of the ‘guilt by association’ principle. We sought to provide a unified explanation for the performance of gene function prediction algorithms in exploiting network structure and thereby simplify future analysis.

Results: We use co-expression networks to show that most exploited network structure simply reconstructs the original correlation matrices from which the co-expression network was obtained. We show the same principle works in predicting gene function in protein interaction networks and that these methods perform comparably to much more sophisticated gene function prediction algorithms.

Availability and implementation: Data and algorithm implementation are fully described and available at http://www.chibi.ubc.ca/extended. Programs are provided in Matlab m-code.

Contact:  paul@chibi.ubc.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast
Authors: Dai Zhiming , Dai Xianhua , Xiang Qian
Published: May 2011

Motivation: The intrinsic DNA sequence is an important determinant of nucleosome positioning. Some DNA sequence patterns can facilitate nucleosome formation, while others can inhibit nucleosome formation. Nucleosome positioning influences the overall rate of sequence evolution. However, its impacts on specific patterns of sequence evolution are still poorly understood.

Results: Here, we examined whether nucleosomal DNA and nucleosome-depleted DNA show distinct polymorphism patterns to maintain adequate nucleosome architecture on a genome scale in yeast. We found that sequence polymorphisms in nucleosomal DNA tend to facilitate nucleosome formation, whereas polymorphisms in nucleosome-depleted DNA tend to inhibit nucleosome formation, which is especially evident at nucleosome-disfavored sequences in nucleosome-free regions at both ends of genes. Sequence polymorphisms facilitating nucleosome positioning correspond to stable nucleosome positioning. These results reveal that sequence polymorphisms are under selective constraints to maintain nucleosome positioning.

Contact:  zhimdai@gmail.com; issdxh@mail.sysu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences
Authors: Lee Tzong-Yi , Lin Zong-Qing , Hsieh Sheng-Jen , Bretaña Neil Arvin , Lu Cheng-Tsung
Published: May 2011

Summary: Bioinformatics research often requires conservative analyses of a group of sequences associated with a specific biological function (e.g. transcription factor binding sites, micro RNA target sites or protein post-translational modification sites). Due to the difficulty in exploring conserved motifs on a large-scale sequence data involved with various signals, a new method, MDDLogo, is developed. MDDLogo applies maximal dependence decomposition (MDD) to cluster a group of aligned signal sequences into subgroups containing statistically significant motifs. In order to extract motifs that contain a conserved biochemical property of amino acids in protein sequences, the set of 20 amino acids is further categorized according to their physicochemical properties, e.g. hydrophobicity, charge or molecular size. MDDLogo has been demonstrated to accurately identify the kinase-specific substrate motifs in 1221 human phosphorylation sites associated with seven well-known kinase families from Phospho.ELM. Moreover, in a set of plant phosphorylation data-lacking kinase information, MDDLogo has been applied to help in the investigation of substrate motifs of potential kinases and in the improvement of the identification of plant phosphorylation sites with various substrate specificities. In this study, MDDLogo is comparable with another well-known motif discover tool, Motif-X.

Contact:  francis@saturn.yzu.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
An Evaluation of Using Population Pharmacokinetic Models to Estimate Pharmacodynamic Parameters for Propofol and Bispectral Index in Children
Authors: Coppens Marc J. , Eleveld Douglas J. , Proost Johannes H. , Marks Luc A. M. , Van Bocxlaer Jan F. P. , Vereecke Hugo , Absalom Anthony R. , Struys Michel M. R. F.
Published: May 2011

Background

To study propofol pharmacodynamics in a clinical setting a pharmacokinetic model must be used to predict drug plasma concentrations. Some investigators use a population pharmacokinetic model from existing literature and minimize the pharmacodynamic objective function. The purpose of the study was to determine whether this method selects the best-performing pharmacokinetic model in a set and provides accurate estimates of pharmacodynamic parameters in models for bispectral index in children after propofol administration.

Methods

Twenty-eight children classified as American Society of Anesthesiologists physical status 1 who were given general anesthesia for dental treatment were studied. Anesthesia was given using target-controlled infusion of propofol based on the Kataria model. Propofol target plasma concentration was 7 μg/ml for 15 min, followed by 1 μg/ml for 15 min or until signs of awakening, followed by 5 μg/ml for 15 min. Venous blood samples were taken 1, 2, 5, 10, and 15 min after each change in target. A classic pharmacokinetic-pharmacodynamic model was estimated, and the methodology of other studies was duplicated using pharmacokinetic models from the literature and (re-)estimating the pharmacodynamic models.

Results

There is no clear relationship between pharmacokinetic precision and the pharmacodynamic objective function. Low pharmacodynamic objective function values are not associated with accurate estimation of the pharmacodynamic parameters when the pharmacokinetic model is taken from other sources.

Conclusion

Minimization of the pharmacodynamic objective function does not select the most accurate pharmacokinetic model. Using population pharmacokinetic models from the literature instead of the 'true' pharmacokinetic model can lead to better predictions of bispectral index while incorrectly estimating the pharmacodynamic parameters.
Spinal Anesthesia in Infant Rats
Authors: Yahalom Barak , Athiraman Umeshkumar , Soriano Sulpicio G. , Zurakowski David , Carpino Elizabeth A. , Corfas Gabriel , Berde Charles B.
Published: May 2011

Background

Previous studies in infant rats and case-control studies of human infants undergoing surgery have raised concerns about potential neurodevelopmental toxicities of general anesthesia. Spinal anesthesia is an alternative to general anesthesia for some infant surgeries. To test for potential toxicity, a spinal anesthesia model in infant rats was developed.

Methods

Rats of postnatal ages 7, 14, and 21 days were assigned to no treatment, 1% isoflurane for either 1 h or 6 h, or lumbar spinal injection of saline or bupivacaine at doses of 3.75 mg/kg (low dose) or 7.5 mg/kg (high dose). Subgroups of animals underwent neurobehavioral testing and blood gas analysis. Brain and lumbar spinal cord sections were examined for apoptosis using cleaved caspase-3 immunostaining. The lumbar spinal cord was examined histologically.Rats exposed to spinal or general anesthesia as infants underwent Rotarod testing of motor performance as adults. Data were analyzed using ANOVA with general linear models, Friedman tests, and Mann-Whitney U tests, as appropriate.

Results

Bupivacaine 3.75 mg/kg was effective for spinal anesthesia in all age groups. Impairments in sensory and motor function recovered in 40-60 min. Blood gases were similar among groups. Brain and spinal cord apoptosis increased in rats receiving 6 h of 1% isoflurane, but not among the other treatments. All groups showed intact motor performance at adulthood.

Conclusions

Spinal anesthesia is technically feasible in infant rats and appears benign in terms of neuroapoptotic and neuromotor sequelae.
Infectious Complications in Pediatric Acute Liver Failure
Authors: Godbole Gauri , Shanmugam Naresh , Dhawan Anil , Verma Anita
Published: May 2011

Objectives:

Acute liver failure (ALF) is rare in children but carries high mortality. Infectious complications (IC) in adults are an important cause of mortality; however, there are few data in the pediatric population. The aim of the study was to determine the incidence of IC and their effects on the outcome in children with ALF.

Materials and Methods:

The present study is a retrospective review of the case records of children presenting with ALF to our center. All patients with ALF received antibiotics and antifungal as prophylaxis from day 1 and high‐dose acyclovir was given to neonates only (stopped when herpes simplex was ruled out). Biochemical parameters, duration of ventilation and intensive care, overall hospital stay, and patient outcome were compared between patients with IC and non‐IC.

Results:

A total of 145 children (78 boys), median (range) age 4.22 (1 day–16 years) years, were studied. Thirty‐seven of 145 (25%) patients had proven IC. The predominant infections included 14 episodes of bacteremia in 13 patients and lower respiratory tract infection and urinary tract infection in 10 and 8 patients, respectively. IC occurred in patients after a median (range) duration of 16 (0–54) days of admission. Median (range) duration of hospital stay in patients with IC was 38 (1–201) days and was significantly higher than in those without IC (10 [1–74] days), P < 0.0001. Overall mortality was 21% (31), of which 7% (11) was from the IC group and 14% (20) from the non‐IC group; the difference was not statistically significant.

Conclusions:

Infections were more frequent after 2 weeks of admission. Patients with sepsis had longer hospital stays and prolonged ventilation. Invasive fungal infections were rare in pediatric ALF with adequate doses of antifungal prophylaxis.
Consistent avoidance of human disturbance over large geographical distances by a migratory bird
Authors: Végvári Zsolt , Barta Zoltán , Mustakallio Pekka , Székely Tamás
Published: May 2011

Recent work on animal personalities has demonstrated that individuals may show consistent behaviour across situations and contexts. These studies were often carried out in one location and/or during short time intervals. Many animals, however, migrate and spend their life in several geographically distinct locations, and they may either adopt behaviours specific to the local environment or keep consistent behaviours over ecologically distinct locations. Long-distance migratory species offer excellent opportunities to test whether the animals maintain their personalities over large geographical scale, although the practical difficulties associated with these studies have hampered such tests. Here, we demonstrate for the first time consistency in disturbance tolerance behaviour in a long-distance migratory bird, using the common craneGrus grusas an ecological model species. Cranes that hatched in undisturbed habitats in Finland choose undisturbed migratory stop-over sites in Hungary, 1300–2000 km away from their breeding ground. This is remarkable, because these sites are not only separated by large distances, they also differ ecologically: the breeding sites are wooded bogs and subarctic tundra, whereas the migratory stop-over sites are temperate zone alkaline grasslands. The significance of our study goes beyond evolutionary biology and behavioural ecology: local effects on behaviour may carry over large distances, and this hitherto hidden implication of habitat selection needs to be incorporated into conservation planning.
Leeches run cold, then hot
Authors: Petersen Ann M. , Chin Wendy , Feilich Kara L. , Jung Grace , Quist Jessica L. , Wang Jasmine , Ellerby David J.
Published: May 2011

Food processing is costly, potentially limiting the energy and time devoted to other essential functions such as locomotion or reproduction. In ectotherms, post-prandial thermophily, the selection of a warm environmental temperature after feeding, may be advantageous in minimizing the duration of this elevated cost. Although present in many vertebrate taxa, this behaviour had not previously been observed in invertebrates. Sanguivorous leeches ingest large blood meals that are costly to process and limit mobility until excess fluid can actively be expelled to reduce body volume. When presented with a temperature gradient from 10°C to 30°C, leeches select a temperature that is significantly warmer (24.3 ± 0.9°C,n= 6) than their acclimation temperature (Ta, 21°C). Unfed leeches preferred temperatures that were significantly cooler than ambient (12.8 ± 0.9°C,n= 6). This behavioural strategy is consistent with minimizing the time course of elevated post-feeding energy costs and reducing energy expenditure during fasting. Our observations raise the possibility that thermoregulatory behaviour of this type is an unrecognized feature of other invertebrate taxa.
Methylorosula polaris gen. nov., sp. nov., an aerobic, facultatively methylotrophic psychrotolerant bacterium from tundra wetland soil
Authors: Berestovskaya Julia Ju. , Kotsyurbenko Oleg R. , Tourova Tatyana P. , Kolganova Tatyana V. , Doronina Nina V. , Golyshin Peter N. , Vasilyeva Lina V.
Published: May 2011

Three strains of Gram-negative, aerobic, motile bacteria with bipolar flagella were isolated from acidic tundra wetland soils near the city of Vorkuta and from the Chukotka and Yugorsky Peninsulas and designated strains V-022T, Ch-022 and Ju-022. The cells were rod-shaped, 0.5–0.6 µm in width and 1.3–4.5 µm in length and reproduced by irregular fission. These bacteria were facultative methylotrophs that used methanol, methylamines and a wide range of other sources of carbon and energy such as sugars and polysaccharides, ethanol and amino acids. The isolates used the Calvin–Benson pathway for the assimilation of one-carbon compounds and were unable to fix nitrogen. The new strains were moderately acidophilic and psychrotolerant, capable of growth over a pH range of 4.0 to 7.8, with optimum growth at pH 5.5–6.0. Growth occurred between 4 and 30 °C (optimum 20–25 °C). The principal phospholipid fatty acid was C18 : 1ω7c. The DNA G+C content of strain V-022Twas 65.2 mol%. Analysis of the 16S rRNA gene sequences revealed that all three isolates V-022T, Ch-022 and Yu-022 exhibited almost identical 16S rRNA gene sequences (99.9 % gene sequence similarity) and formed a new lineage within the classAlphaproteobacteria. The nameMethylorosula polarisis suggested to accommodate this new genus and novel species with strain V-022T( = DSM 22001T = VKM V-2485T) as the type strain of the type species.
Devosia psychrophila sp. nov. and Devosia glacialis sp. nov., from alpine glacier cryoconite, and an emended description of the genus Devosia
Authors: Zhang De-Chao , Redzic Mersiha , Liu Hong-Can , Zhou Yu-Guang , Schinner Franz , Margesin Rosa
Published: May 2011

Two psychrophilic strains, Cr7-05T and Cr4-44T, isolated from alpine glacier cryoconite, were characterized by using a polyphasic approach. Both strains were psychrophilic, showing good growth over a temperature range of 1–20 °C. The chemotaxonomic characteristics of these isolates included the presence of C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major cellular fatty acids, Q-10 as the predominant ubiquinone and diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids as major polar lipids. The DNA G+C contents of strains Cr7-05T and Cr4-44T were 61.4 and 63.6 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belong to the genus Devosia. The 16S rRNA gene sequence similarity between the two strains was 98.6 %, but DNA–DNA hybridization indicated 54 % relatedness. Strains Cr7-05T and Cr4-44T exhibited 16S rRNA gene sequence similarity of 94.7–97.2 and 94.9–96.9 %, respectively, to the type strains of recognized Devosia species. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strains Cr7-05T and Cr4-44T represent two novel species within the genus Devosia, for which the names Devosia psychrophila sp. nov. (type strain Cr7-05T  = DSM 22950T  = CGMCC 1.10210T  = CIP 110130T) and Devosia glacialis sp. nov. (type strain Cr4-44T  = CGMCC 1.10691T  = LMG 26051T) are proposed. An emended description of the genus Devosia is also provided.
Sphingobium lucknowense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from HCH-contaminated soil
Authors: Garg Nidhi , Bala Kiran , Lal Rup
Published: May 2011

A yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterium, designated F2T, was isolated from an HCH dumpsite at Ummari village in Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Sphingobium. Its closest neighbour was Sphingobium japonicum UT26T (99.2 % 16S rRNA gene sequence similarity). The DNA G+C content was 65.7 mol%. The polyamine profile showed the presence of spermidine. The respiratory pigment was ubiquinone Q-10. The predominant cellular fatty acids were C16 : 0 (12.5 %), C14 : 0 2-OH (8.1 %), summed feature 3 (consisting of C16 : 1ω7c and/or C16 : 1ω6c; 5.8 %) and summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c; 53.1 %). The major polar lipids of strain F2T were phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid. DNA–DNA relatedness and biochemical and physiological characters clearly distinguished the isolate from its closest phylogenetic neighbours. Thus, strain F2T represents a novel species of the genus Sphingobium, for which the name Sphingobium lucknowense sp. nov. is proposed. The type strain is strain F2T ( = MTCC 9456T  = CCM 7544T).
Tropicimonas aquimaris sp. nov., isolated from seawater, and emended description of the genus Tropicimonas Harwati et al. 2009
Authors: Oh Ki-Hoon , Choi Won-Chan , Jung Yong-Taek , Kang So-Jung , Oh Tae-Kwang , Yoon Jung-Hoon
Published: May 2011

A Gram-staining-negative, aerobic, non-motile and rod-shaped bacterial strain, designated DPG-21T, was isolated from seawater from the South Sea in Korea, and investigated using a polyphasic taxonomic approach. Strain DPG-21T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In a neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain DPG-21T clustered with Tropicimonas isoalkanivorans B51T (with a sequence similarity of 97.1 %); the novel strain showed lower 16S rRNA gene sequence similarities (<95.4 %) with the other species included in the tree. The mean DNA–DNA relatedness value between strain DPG-21T and T. isoalkanivorans DSM 19548T was 12 %. The predominant ubiquinones of strain DPG-21T were Q-10 and Q-9 while C18 : 1ω7c was the strain’s major fatty acid. The polar lipid profile of strain DPG-21T was similar to that of T. isoalkanivorans DSM 19548T. The genomic DNA G+C content of the novel strain was 69.6 mol%. Some phenotypic properties and the phylogenetic and genetic data indicated that strain DPG-21T was distinct from T. isoalkanivorans and represents a novel species of the genus Tropicimonas, for which the name Tropicimonas aquimaris sp. nov. is proposed. The type strain is DPG-21T ( = KCTC 23424T = CCUG 60524T).
Pontibacter populi sp. nov., isolated from the soil of a Euphrates poplar (Populus euphratica) forest
Authors: Xu Mengbo , Wang Yang , Dai Jun , Jiang Fan , Rahman Erkin , Peng Fang , Fang Chengxiang
Published: May 2011

A Gram-negative-staining, rod-shaped, non-motile and pink bacterial strain was isolated from the soil of a Populus euphratica forest located in Xinjiang, China. The strain, designated strain HYL7-15T, was subjected to a taxonomic analysis using a polyphasic approach. 16S rRNA gene sequence analyses indicated that the isolate belonged to the phylum Bacteroidetes and was related to the genus Pontibacter, with sequence similarities ranging from 93.1 to 95.0 % with other species of the genus Pontibacter. Strain HYL7-15T contained MK-7 as the predominant menaquinone and its DNA G+C content was 44.9 mol%. The major cellular fatty acids of the novel strain were iso-C15 : 0 (16.49 %), iso-C17 : 0 3-OH (10.96 %) and summed feature 4 (comprising anteiso-C17 : 1 B and/or iso-C17 : 1 I, 18.46 %). The major polar lipids were phosphatidylethanolamine (PE) and phosphatidylglycerol (PG); diphosphatidylglycerol (DPG), three unknown aminophospholipids (APLs) and two unknown phospholipids (PLs) were also detected. On the basis of the evidence presented, it is concluded that strain HYL7-15T represents a novel species of the genus Pontibacter, for which the name Pontibacter populi sp. nov. is proposed. The type strain is HYL7-15T ( = CCTCC AB 206239T = NRRL B-59488T).
Aquabacterium limnoticum sp. nov., isolated from a freshwater spring
Authors: Chen Wen-Ming , Cho Nian-Tsz , Yang Shwu-Harn , Arun A. B. , Young Chiu-Chung , Sheu Shih-Yi
Published: May 2011

A Gram-negative, facultatively anaerobic, short-rod-shaped, non-motile and non-spore-forming bacterial strain, designated ABP-4T, was isolated from a freshwater spring in Taiwan and was characterized using the polyphasic taxonomy approach. Growth occurred at 20–40 °C (optimum, 30–37 °C), at pH 7.0–10.0 (optimum, pH 7.0–9.0) and with 0–3 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ABP-4T, together with Aquabacterium fontiphilum CS-6T (96.4 % sequence similarity), Aquabacterium commune B8T (96.1 %), Aquabacterium citratiphilum B4T (95.5 %) and Aquabacterium parvum B6T (94.7 %), formed a deep line within the order Burkholderiales. Strain ABP-4T contained summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), C18 : 1 ω7c and C16 : 0 as predominant fatty acids. The major cellular hydroxy fatty acid was C10 : 0 3-OH. The major isoprenoid quinone was Q-8 and the DNA G+C content was 68.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and several uncharacterized phospholipids. The DNA–DNA relatedness of strain ABP-4T with respect to recognized species of the genus Aquabacterium was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain ABP-4T represents a novel species in the genus Aquabacterium, for which the name Aquabacterium limnoticum sp. nov. is proposed. The type strain is ABP-4T ( = BCRC 80167T = KCTC 23306T).
Nocardia grenadensis sp. nov., isolated from sand of the Caribbean Sea
Authors: Kämpfer Peter , Lodders Nicole , Grün-Wollny Iris , Martin Karin , Busse Hans-Jürgen
Published: May 2011

A Gram-stain-positive, non-spore-forming bacterium (GW5-5797T) was isolated on soil extract agar from sand collected at a depth of 5 m in the Caribbean Sea near Grenada. 16S rRNA gene sequence analysis and similarity studies showed that strain GW5-5797T belongs to the genus Nocardia, and is most closely related to Nocardia speluncae N2-11T (99.2 % similarity) and Nocardia jinanensis 04-5195T (99.2 %) and more distantly related to Nocardia rhamnosiphila 202GMOT (98.6 %) and other Nocardia species. Strain GW5-5797T could be distinguished from all other recognized Nocardia species by sequence similarity values less than 98.5 %. The peptidoglycan diamino acid was meso-diaminopimelic acid. Strain GW5-5797T exhibited a quinone system with the predominant compounds MK-8(H4ω-cyclo) and MK-8(H2). The polar lipid profile of GW5-5797T consisted of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid, moderate amounts of phosphatidylinositol and a phosphatidylinositol mannoside and minor amounts of several lipids including a second phosphatidylinositol mannoside. The polyamine pattern contained the major compound spermine and moderate amounts of spermidine. The major fatty acids were C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0. These chemotaxonomic traits are in excellent agreement with those of other Nocardia species. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW5-5797T from the most closely related species, showing 16S rRNA gene sequence similarities >98.5 %. Strain GW5-5797T therefore merits separate species status, and we propose the name Nocardia grenadensis sp. nov., with the type strain GW5-5797T ( = CCUG 60970T  = CIP 110294T).
Description of Belnapia rosea sp. nov. and emended description of the genus Belnapia Reddy et al. 2006
Authors: Jin Rong , Su Jing , Liu Hong-Yu , Wei Yu-Zhen , Li Qiu-Ping , Zhang Yu-Qin , Yu Li-Yan
Published: May 2011

A novel alphaproteobacterial strain, designated CPCC 100156T, was isolated from a forest soil sample collected from Hainan Island, South China, and subjected to taxonomic investigation using a polyphasic approach. The pink- to rosy-coloured colonies on TSA and YM agar were smooth and moist. Good growth occurred at 28–32 °C and at pH 7.0–7.5. The respiratory quinone was ubiquinone-9. The polar lipids consisted of phosphatidylcholine (PC), hydroxyphosphatidylethanolamine (OH-PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and two unidentified aminolipids (AL1, AL2), with a minor amount of ninhydrin-positive phosphoglycolipid. (NPG). The major cellular fatty acids were summed feature 8 (C18 : 1ω7c /C18 : 1ω6c) (49.5 %), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) (22.5 %), and C16 : 0 (14.0 %). The G+C content of the genomic DNA was 70.3 mol%. The organism showed 16S rRNA gene sequence similarity of 97.37 % with Belnapia moabensis DSM 16746T. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolate belonged to the family Acetobacteraceae and consistently formed a robust cluster with Belnapia moabensis DSM 16746T in the phylogenetic tree. The DNA–DNA hybridization value between the new isolate and Belnapia moabensis DSM 16746T was 45.6 %. On the basis of the taxonomic evidence, it is proposed that strain CPCC 100156T represents a novel species, for which the name Belnapia rosea sp. nov. is proposed. The type strain is CPCC 100156T ( = DSM 23312T = CGMCC 1.10758T). The description of the genus Belnapia is emended accordingly.
Mongoliitalea lutea gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a haloalkaline lake
Authors: Yang C. X. , Liu Y. P. , Bao Q. H. , Feng F. Y. , Liu H. R. , Zhang X. J. , Zhao Y. L.
Published: May 2011

Two bacterial isolates from the surface water of a haloalkaline lake on the Mongolia Plateau, strains MIM18T and MIM19, were characterized; their morphological, physiological and chemotaxonomic characters, and phylogenetic position based on 16S rRNA gene sequences, were determined. The two strains were alkaliphilic, halotolerant, non-motile, aerobic, Gram-negative, orange-red, rod-shaped and oxidase-positive. Growth was observed in 0–5.5 % (w/v) NaCl, with optimum growth at 1 %. The temperature range for growth was 0–41 °C, with good growth at 28–37 °C and optimum growth at 30–33 °C. The DNA G+C content was 39.8–41.2 mol%. The strains contained menaquinone MK-7 as the major respiratory quinone and phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. Predominant cellular fatty acids were iso-C15 : 0 (28.1–29.3 %), iso-C17 : 0 3-OH (14.6–18.8 %), C15 : 1ω6c (5.3–8.6 %), C14 : 0 2-OH and/or iso-C15 : 0 2-OH (5.4–6.1 %), and iso-C17 : 1ω9c and/or C16 : 0 10-methyl (5.0–6.8 %). 16S rRNA gene sequence analysis showed that Belliella and Nitritalea of the family Cyclobacteriaceae were the closest related species with sequence similarities of 91.7–92.3 % and 88.2 %, respectively, with strains of these genera; other members of the Cyclobacteriaceae had sequence similarities lower than 88 %. Phylogenetic analysis indicated that the strains formed a deep-rooted lineage distinct from the clades represented by the genera Belliella, Nitritalea, Indibacter, Aquiflexum, Echinicola, Litoribacter, Cyclobacterium and Algoriphagus. Based on the phenotypic and phylogenetic characteristics mentioned above, the two strains are representatives of a single novel species in a new genus; the name Mongoliitalea lutea gen. nov., sp. nov. is proposed, with MIM18T ( = ACCC 05421T = KCTC 23224T) as the type strain.
Psychrobacter isolates of human origin, other than Psychrobacter phenylpyruvicus, are predominantly Psychrobacter faecalis and Psychrobacter pulmonis, with emended description of P. faecalis
Authors: Deschaght Pieter , Janssens Michèle , Vaneechoutte Mario , Wauters Georges
Published: May 2011

Human Psychrobacter isolates, other than Psychrobacter phenylpyruvicus, are predominantly designated Psychrobacter immobilis. Phenotypic and genotypic testing of Psychrobacter isolates that have been deposited in different culture collections as P. immobilis indicates that most of these human isolates belong to the species Psychrobacter faecalis and Psychrobacter pulmonis.
Clathrin Mediates Endocytosis and Polar Distribution of PIN Auxin Transporters inArabidopsis
Authors: Kitakura Saeko , Vanneste Steffen , Robert Stéphanie , Löfke Christian , Teichmann Thomas , Tanaka Hirokazu , Friml Jiří
Published: May 2011

Endocytosis is a crucial mechanism by which eukaryotic cells internalize extracellular and plasma membrane material, and it is required for a multitude of cellular and developmental processes in unicellular and multicellular organisms. In animals and yeast, the best characterized pathway for endocytosis depends on the function of the vesicle coat protein clathrin. Clathrin-mediated endocytosis has recently been demonstrated also in plant cells, but its physiological and developmental roles remain unclear. Here, we assessed the roles of the clathrin-mediated mechanism of endocytosis in plants by genetic means. We interfered with clathrin heavy chain (CHC) function through mutants and dominant-negative approaches in Arabidopsis thaliana and established tools to manipulate clathrin function in a cell type–specific manner. The chc2 single mutants and dominant-negative CHC1 (HUB) transgenic lines were defective in bulk endocytosis as well as in internalization of prominent plasma membrane proteins. Interference with clathrin-mediated endocytosis led to defects in constitutive endocytic recycling of PIN auxin transporters and their polar distribution in embryos and roots. Consistent with this, these lines had altered auxin distribution patterns and associated auxin transport-related phenotypes, such as aberrant embryo patterning, imperfect cotyledon specification, agravitropic growth, and impaired lateral root organogenesis. Together, these data demonstrate a fundamental role for clathrin function in cell polarity, growth, patterning, and organogenesis in plants.
The Jasmonate-ZIM-Domain Proteins Interact with the WD-Repeat/bHLH/MYB Complexes to Regulate Jasmonate-Mediated Anthocyanin Accumulation and Trichome Initiation inArabidopsis thaliana
Authors: Qi Tiancong , Song Susheng , Ren Qingcuo , Wu Dewei , Huang Huang , Chen Yan , Fan Meng , Peng Wen , Ren Chunmei , Xie Daoxin
Published: May 2011

Jasmonates (JAs) mediate plant responses to insect attack, wounding, pathogen infection, stress, and UV damage and regulate plant fertility, anthocyanin accumulation, trichome formation, and many other plant developmental processes. Arabidopsis thaliana Jasmonate ZIM-domain (JAZ) proteins, substrates of the CORONATINE INSENSITIVE1 (COI1)–based SCFCOI1 complex, negatively regulate these plant responses. Little is known about the molecular mechanism for JA regulation of anthocyanin accumulation and trichome initiation. In this study, we revealed that JAZ proteins interact with bHLH (Transparent Testa8, Glabra3 [GL3], and Enhancer of Glabra3 [EGL3]) and R2R3 MYB transcription factors (MYB75 and Glabra1), essential components of WD-repeat/bHLH/MYB transcriptional complexes, to repress JA-regulated anthocyanin accumulation and trichome initiation. Genetic and physiological evidence showed that JA regulates WD-repeat/bHLH/MYB complex-mediated anthocyanin accumulation and trichome initiation in a COI1-dependent manner. Overexpression of the MYB transcription factor MYB75 and bHLH factors (GL3 and EGL3) restored anthocyanin accumulation and trichome initiation in the coi1 mutant, respectively. We speculate that the JA-induced degradation of JAZ proteins abolishes the interactions of JAZ proteins with bHLH and MYB factors, allowing the transcriptional function of WD-repeat/bHLH/MYB complexes, which subsequently activate respective downstream signal cascades to modulate anthocyanin accumulation and trichome initiation.
Microtubule-Associated Proteins MAP65-1 and MAP65-2 Positively Regulate Axial Cell Growth in EtiolatedArabidopsisHypocotyls
Authors: Lucas Jessica R. , Courtney Stephanie , Hassfurder Mathew , Dhingra Sonia , Bryant Adam , Shaw Sidney L.
Published: May 2011

The Arabidopsis thaliana MAP65-1 and MAP65-2 genes are members of the larger eukaryotic MAP65/ASE1/PRC gene family of microtubule-associated proteins. We created fluorescent protein fusions driven by native promoters that colocalized MAP65-1 and MAP65-2 to a subset of interphase microtubule bundles in all epidermal hypocotyl cells. MAP65-1 and MAP65-2 labeling was highly dynamic within microtubule bundles, showing episodes of linear extension and retraction coincident with microtubule growth and shortening. Dynamic colocalization of MAP65-1/2 with polymerizing microtubules provides in vivo evidence that plant cortical microtubules bundle through a microtubule-microtubule templating mechanism. Analysis of etiolated hypocotyl length in map65-1 and map65-2 mutants revealed a critical role for MAP65-2 in modulating axial cell growth. Double map65-1 map65-2 mutants showed significant growth retardation with no obvious cell swelling, twisting, or morphological defects. Surprisingly, interphase microtubules formed coaligned arrays transverse to the plant growth axis in dark-grown and GA4-treated light-grown map65-1 map65-2 mutant plants. We conclude that MAP65-1 and MAP65-2 play a critical role in the microtubule-dependent mechanism for specifying axial cell growth in the expanding hypocotyl, independent of any mechanical role in microtubule array organization.
Sumoylation of eukaryotic elongation factor 2 is vital for protein stability and anti‐apoptotic activity in lung adenocarcinoma cells
Authors: Chen Chih‐Yi , Fang Hsin‐Yuan , Chiou Shiow‐Her , Yi Shih‐En , Huang Chih‐Yang , Chiang Shu‐Fen , Chang Hui‐Wen , Lin Tze‐Yi , Chiang I‐Ping , Chow Kuan‐Chih
Published: May 2011

By screening mouse monoclonal antibody libraries for Kelch repeats, we serendipitously identified monoclonal antibodies to eukaryotic elongation factor 2 (eEF2). Interestingly, eEF2 was highly expressed in lung adenocarcinoma (LADC), but not in the neighboring non‐tumor lung tissue. Normally, eEF2 is involved in the peptidyl‐tRNA translocation during protein synthesis. Overexpression of eEF2 would implicate an association with disease progression of LADC. In the present study, we investigated the prognostic significance of eEF2 in patients with LADC. Expression of eEF2 was detected by immunoblotting, immunohistochemistry and confocal immunofluorescence microscopy. Our results show that patients with high eEF2 expression had a significantly higher incidence of early tumor recurrence (67.8%vs18.2%,P = 0.016), and a significantly worse prognosis (P < 0.001). In anin vitrostudy, silencing of eEF2 expression increased mitochondrial elongation, cellular autophagy and cisplatin sensitivity. Moreover, eEF2 was sumoylated in LADC cells, and eEF2 sumoylation correlated with drug resistance. These results suggest that eEF2 is an anti‐apoptotic marker in LADC. However, biological function and involvement of eEF2 in the disease progression of LADC require further studies. (Cancer Sci2011; 102: 1582–1589)
Anabolic Androgenic Steroid Abuse: Multiple Mechanisms of Regulation of GABAergic Synapses in Neuroendocrine Control Regions of the Rodent Forebrain
Authors: Oberlander J. G. , Porter D. M. , Penatti C. A. A. , Henderson L. P.
Published: May 2011

Anabolic androgenic steroids (AAS) are synthetic derivatives of testosterone originally developed for clinical purposes but are now predominantly taken at suprapharmacological levels as drugs of abuse. To date, almost 100 different AAS compounds that vary in metabolic fate and physiological effects have been designed and synthesised. Although they are administered for their ability to enhance muscle mass and performance, untoward side effects of AAS use include changes in reproductive and sexual behaviours. Specifically, AAS, depending on the type of compound administered, can delay or advance pubertal onset, lead to irregular oestrous cyclicity, diminish male and female sexual behaviours, and accelerate reproductive senescence. Numerous brains regions and neurotransmitter signalling systems are involved in the generation of these behaviours, and are potential targets for both chronic and acute actions of the AAS. However, critical to all of these behaviours is neurotransmission mediated by GABAA receptors within a nexus of interconnected forebrain regions that includes the medial preoptic area, the anteroventral periventricular nucleus and the arcuate nucleus of the hypothalamus. We review how exposure to AAS alters GABAergic transmission and neural activity within these forebrain regions, taking advantage of in vitro systems and both wild‐type and genetically altered mouse strains, aiming to better understand how these synthetic steroids affect the neural systems that underlie the regulation of reproduction and the expression of sexual behaviours.
Inhibition of Maternal Behaviour by Central Infusion of Corticotrophin‐Releasing Hormone in Marmoset Monkeys
Authors: Saltzman W. , Boettcher C. A. , Post J. L. , Abbott D. H.
Published: May 2011

Stress can inhibit maternal behaviour and increase rates of child abuse in humans and other animals; however, the neuroendocrine mechanisms are not known. To determine whether corticotrophin‐releasing hormone (CRH) plays a role in stress‐induced disruption of maternal behaviour in primates, we characterised the effects of acute i.c.v. infusions of CRH on maternal and abusive behaviour in common marmoset monkeys (Callithrix jacchus). Nulliparous females were implanted with indwelling i.c.v. guide cannulae before conception. Between 18 and 58 days after the birth of her first infants, each female underwent a series of i.c.v. infusions of human CRH (0, 2, 8 and 25 μg) in 8 μl of artificial cerebrospinal fluid. In the 70 min after infusion, marmosets were tested with one of their infants, first in their home cage and, subsequently, in an unfamiliar cage in which the infant was confined in a transparent box on the cage floor. In the home cage, the highest dose of CRH significantly reduced the amount of time that mothers spent carrying their infants, as compared to vehicle alone, although it did not reliably affect aggression toward the infant or other behaviours. In the confined‐infant test, the highest dose of CRH significantly reduced the amount of time that mothers spent on the cage floor, increased mothers’ vocalisation rates, and tended to reduce their activity levels and time spent in proximity to their infant. Twenty‐five micrograms of CRH also elicited significant elevations in plasma adrenocorticotrophic hormone and cortisol concentrations compared to vehicle. These results indicate that i.c.v.‐administered CRH reduces maternal behaviour in marmoset mothers, in both familiar and unfamiliar environments, but does not increase infant abuse.
The biosynthesis of Caryophyllaceae‐like cyclic peptides in Saponaria vaccaria L. from DNA‐encoded precursors
Authors: Condie Janet A. , Nowak Goska , Reed Darwin W. , Balsevich J. John , Reaney Martin J. T. , Arnison Paul G. , Covello Patrick S.
Published: May 2011

Cyclic peptides (CPs) are produced in a very wide range of taxa. Their biosynthesis generally involves either non‐ribosomal peptide synthases or ribosome‐dependent production of precursor peptides. Plants within the Caryophyllaceae and certain other families produce CPs which generally consist of 5–9 proteinogenic amino acids. The biological roles for these CPs in the plant are not very clear, but many of them have activity in mammalian systems. There is currently very little known about the biosynthesis of CPs in the Caryophyllaceae. A collection of expressed sequence tags from developing seeds of Saponaria vaccaria was investigated for information about CP biosynthesis. This revealed genes that appeared to encode CP precursors which are subsequently cyclized to mature CPs. This was tested and confirmed by the expression of a cDNA encoding a putative precursor of the CP segetalin A in transformed S. vaccaria roots. Similarly, extracts of developing S. vaccaria seeds were shown to catalyze the production of segetalin A from the same putative (synthetic) precursor. Moreover, the presence in S. vaccaria seeds of two segetalins, J [cyclo(FGTHGLPAP)] and K [cyclo(GRVKA)], which was predicted by sequence analysis, was confirmed by liquid chromatography/mass spectrometry. Sequence analysis also predicts the presence of similar CP precursor genes in Dianthus caryophyllus and Citrus spp. The data support the ribosome‐dependent biosynthesis of Caryophyllaceae‐like CPs in the Caryophyllaceae and Rutaceae.