bluuebunny/crossref_metadata_2025 huggingface dataset:
Virgibacillus subterraneus sp. nov., a moderately halophilic Gram-positive bacterium isolated from subsurface saline soil
Authors: Wang Xiaowei , Xue Yanfen , Ma Yanhe
Published: January 2010

A Gram reaction-positive, moderately halophilic bacterium, designated H57B72T, was isolated from subsurface saline soil of Qaidam basin in the Qinghai province, China. Cells were rod-shaped, strictly aerobic, spore-forming and motile. The isolate grew optimally at 9 % (w/v) NaCl, pH 7.5 and 30 °C. The cell-wall peptidoglycan of strain H57B72T contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 (59.97 %) and anteiso-C17 : 0 (17.14 %). Phosphatidylglycerol, diphosphatidylglycerol and a glycolipid were found to be the predominant polar lipids. The genomic DNA G+C content of strain H57B72T was 37.1 mol%. 16S rRNA gene sequence analysis showed that strain H57B72T was a member of the genus Virgibacillus and was most closely related to Virgibacillus salinus DSM 21756T (98.3 % gene sequence similarity). The level of DNA–DNA relatedness between strain H57B72T and V. salinus DSM 21756T was 8.5 %. Based on the phenotypic, genotypic and phylogenetic data presented, strain H57B72T represents a novel species, for which the name Virgibacillus subterraneus sp. nov. is proposed. The type strain is H57B72T (=DSM 22441T =CGMCC 1.7734T).
Acidovorax soli sp. nov., isolated from landfill soil
Authors: Choi Jung-Hye , Kim Min-Soo , Roh Seong Woon , Bae Jin-Woo
Published: January 2010

A Gram-negative, aerobic, rod-shaped, non-motile strain, BL21T, was isolated from landfill soil in Pohang, Korea. Strain BL21T grew optimally at pH 7.0, 30 °C and 0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain BL21T belonged to the class Betaproteobacteria and was related to the genus Acidovorax. The 16S rRNA gene sequence of strain BL21T was less than 98.30 % similar to those of other species in the genus Acidovorax. DNA–DNA hybridization values with phylogenetically related species of the genus Acidovorax were only 11.7–28.4 %. The major fatty acid components included summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c), C16 : 0, C18 : 1
ω7c and C10 : 0 3-OH. The DNA G+C content was 60.9 mol%. For these reasons, strain BL21T (=KCTC 22399T =JCM 15909T) is proposed as a novel species in the genus Acidovorax, with the name Acidovorax soli sp. nov.
Streptomyces tateyamensis sp. nov., Streptomyces marinus sp. nov. and Streptomyces haliclonae sp. nov., isolated from the marine sponge Haliclona sp.
Authors: Khan Shams Tabrez , Tamura Tomohiko , Takagi Motoki , Shin-ya Kazuo
Published: January 2010

Three Gram-positive, NaCl-requiring actinobacteria were isolated from a marine sponge, Haliclona sp., collected from the coast of Tateyama City, Japan. Comparison of 16S rRNA gene sequences indicated that these strains represent novel members of the genus Streptomyces, exhibiting low 16S rRNA gene sequence similarities of 98.3–97.4 % with recognized members of the genus. The cell hydrolysates contained the LL-isomer of diaminopimelic acid and the predominant quinones were MK-9 (H6 and/or H8). The DNA G+C contents were in the range 72–75 mol%. A polyphasic study of the strains and comparison of the characters with related species of the genus show that these strains represent three novel species of the genus Streptomyces. Therefore, the names Streptomyces tateyamensis sp. nov., Streptomyces haliclonae sp. nov. and Streptomyces marinus sp. nov. are proposed for strains Sp080513SC-30T (=NBRC 105048T =DSM 41969T), Sp080513SC-31T (=NBRC 105049T =DSM 41970T) and Sp080513GE-26T (=NBRC 105047T =DSM 41968T), respectively.
Methylocapsa aurea sp. nov., a facultative methanotroph possessing a particulate methane monooxygenase, and emended description of the genus Methylocapsa
Authors: Dunfield Peter F. , Belova Svetlana E. , Vorob'ev Alexey V. , Cornish Sabrina L. , Dedysh Svetlana N.
Published: January 2010

An aerobic, methanotrophic bacterium, designated KYGT, was isolated from a forest soil in Germany. Cells of strain KYGT were Gram-negative, non-motile, slightly curved rods that multiplied by binary fission and produced yellow colonies. The cells contained intracellular granules of poly-β-hydroxybutyrate at each cell pole, a particulate methane monooxygenase (pMMO) and stacks of intracytoplasmic membranes (ICMs) packed in parallel along one side of the cell envelope. Strain KYGT grew at pH 5.2–7.2 and 2–33 °C and could fix atmospheric nitrogen under reduced oxygen tension. The major cellular fatty acid was C18 : 1
ω7c (81.5 %) and the DNA G+C content was 61.4 mol%. Strain KYGT belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and was most closely related to the obligate methanotroph Methylocapsa acidiphila B2T (98.1 % 16S rRNA gene sequence similarity and 84.7 % pmoA sequence similarity). Unlike Methylocapsa acidiphila B2T, which grows only on methane and methanol, strain KYGT was able to grow facultatively on acetate. Facultative acetate utilization is a characteristic of the methanotrophs of the genus Methylocella, but the genus Methylocella does not produce pMMO or ICMs. Strain KYGT differed from Methylocapsa acidiphila B2T on the basis of substrate utilization pattern, pigmentation, pH range, cell ultrastructure and efficiency of dinitrogen fixation. Therefore, we propose a novel species, Methylocapsa aurea sp. nov., to accommodate this bacterium. The type strain is KYGT (=DSM 22158T =VKM B-2544T).
Terrimonas aquatica sp. nov., isolated from a freshwater spring
Authors: Sheu Shih-Yi , Cho Nian-Tsz , Arun A. B. , Chen Wen-Ming
Published: January 2010

A yellow-pigmented bacterial strain, designated RIB1-6T, was isolated from a freshwater spring in Taiwan. Strain RIB1-6T was aerobic, Gram-negative, rod-shaped, non-motile and non-spore-forming. Growth occurred at 10–37 °C, at pH 7–8 and with 0–1 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain RIB1-6T belonged to the genus Terrimonas and its two closest neighbours were Terrimonas ferruginea ATCC 13524T and Terrimonas lutea DYT (16S rRNA gene sequence similarity 97.4 % and 93.5 %, respectively). Strain RIB1-6T contained iso-C15 : 0 (33.4 %), iso-C17 : 0 3-OH (18.2 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c; 14.7 %) and iso-C15 : 1 (11.5 %) as the predominant fatty acids. The major isoprenoid quinone was MK-7. The DNA G+C content of strain RIB1-6T was 47.3 mol%. On the basis of the genotypic and phenotypic data, strain RIB1-6T represents a novel species in the genus Terrimonas, for which the name Terrimonas aquatica sp. nov. is proposed. The type strain is RIB1-6T (=BCRC 17941T=LMG 24825T).
Differentiation of Bifidobacterium species using partial RNA polymerase β-subunit (rpoB) gene sequences
Authors: Kim Byoung Jun , Kim Hee-Youn , Yun Yeo-Jun , Kim Bum-Joon , Kook Yoon-Hoh
Published: January 2010

Partial RNA polymerase β-subunit gene (rpoB) sequences (315 bp) were determined and used to differentiate the type strains of 23 species of the genus Bifidobacterium. The sequences were compared with those of the partial hsp60 (604 bp) and 16S rRNA genes (1475 or 1495 bp). The rpoB gene sequences showed nucleotide sequence similarities ranging from 84.1 % to 99.0 %, while the similarities of the hsp60 sequences ranged from 78.5 % to 99.7 % and the 16S rRNA gene sequence similarities ranged from 89.4 % to 99.2 %. The phylogenetic trees constructed from the sequences of these three genes showed similar clustering patterns, with the exception of several species. The Bifidobacterium catenulatum–Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum subsp. pseudolongum–Bifidobacterium pseudolongum subsp. globosum and Bifidobacterium gallinarum–Bifidobacterium pullorum–Bifidobacterium saeculare groups were more clearly differentiated in the partial rpoB and hsp60 gene sequence trees than they were in the 16S rRNA gene tree. Based on sequence similarities and tree topologies, the newly determined rpoB gene sequences are suitable molecular markers for the differentiation of species of the genus Bifidobacterium and support various other molecular tools used to determine the relationships among species of this genus.
Dongia mobilis gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a sequencing batch reactor for treatment of malachite green effluent
Authors: Liu Ying , Jin Jing-Hua , Liu Ying-Hao , Zhou Yu-Guang , Liu Zhi-Pei
Published: January 2010

A Gram-negative, strictly aerobic and heterotrophic, non-spore-forming bacterial strain, designated LM22T, was isolated from activated sludge of a sequencing batch reactor for the treatment of malachite green effluent. Cells of strain LM22Twere slightly curved to straight rods (0.3–0.5×0.6–1.0 μm) and motile by a single polar flagellum. Strain LM22Twas negative for oxidase and catalase activities and phototrophic growth. An internal membrane system and bacteriochlorophyllawere absent. Growth occurred at 20–40 °C (optimum 30–35 °C) and pH 6.0–10.0 (optimum pH 7.0–7.5). Strain LM22Tdid not require NaCl for growth and tolerated up to 2.0 % NaCl (optimum 0.5 %). The major ubiquinone was Q-10. The major fatty acids (>10 % of the total) were C18 : 1ω7c(32.9 %), C19 : 0cycloω8c(18.7 %), C16 : 0(12.1 %) and C16 : 02-OH (10.5 %). Phylogenetic analysis of 16S rRNA gene sequences showed thatInquilinus limosusAU0476Twas the closest relative (90.4 % 16S rRNA gene sequence similarity). The DNA G+C content was 65.6 mol%. On basis of phenotypic, chemotaxonomic and phylogenetic data, strain LM22Twas considered to represent a novel genus and species of the familyRhodospirillaceae, for which the nameDongia mobilisgen. nov., sp. nov. is proposed. The type strain ofDongia mobilisis LM22T(=CGMCC 1.7660T=JCM 15798T).
Sphingobium qiguonii sp. nov., a carbaryl-degrading bacterium isolated from a wastewater treatment system
Authors: Yan Qiu-Xiang , Wang Yong-Xia , Li Shun-Peng , Li Wen-Jun , Hong Qing
Published: January 2010

A Gram-staining-negative, catalase-positive, carbaryl-degrading, non-spore-forming, non-motile, rod-shaped bacterium, designated strain X23T, was isolated from a wastewater treatment system. Phylogenetic analysis based on 16S rRNA gene sequence indicated that the strain belongs to the genus Sphingobium. The highest 16S rRNA gene sequence similarity observed for the isolate was 96.6 % with the type strain of Sphingobium amiense. Chemotaxonomic data [major ubiquinone: Q-10; major polar lipids: diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine and unknown aminolipids and phospholipids; major fatty acids: summed feature 7 (C18 : 1
ω7c, C18 : 1
ω9t and/or C18 : 1
ω12t), C16 : 1
ω5c, C14 : 0 2-OH and C16 : 0 2-OH] as well as the inability to reduce nitrate and the presence of spermidine as the major polyamine supported the affiliation of the strain to the genus Sphingobium. Based on the phylogenetic analysis, whole-cell fatty acid composition and biochemical characteristics, the strain could be separated from all recognized species of the genus Sphingobium. Strain X23T should be classified as a novel species of the genus Sphingobium, for which the name Sphingobium qiguonii sp. nov. is proposed, with strain X23T (=CCTCC AB 208221T =DSM 21541T) as the type strain.
Halomonas titanicae sp. nov., a halophilic bacterium isolated from the RMS Titanic
Authors: Sánchez-Porro Cristina , Kaur Bhavleen , Mann Henrietta , Ventosa Antonio
Published: January 2010

A Gram-negative, heterotrophic, aerobic, non-endospore-forming, peritrichously flagellated and motile bacterial strain, designated BH1T, was isolated from samples of rusticles, which are formed in part by a consortium of micro-organisms, collected from the RMS Titanic wreck site. The strain grew optimally at 30–37 °C, pH 7.0–7.5 and in the presence of 2–8 % (w/v) NaCl. We carried out a polyphasic taxonomic study in order to characterize the strain in detail. Phylogenetic analyses based on 16S rRNA gene sequence comparison indicated that strain BH1T clustered within the branch consisting of species of Halomonas. The most closely related type strains were Halomonas neptunia (98.6 % 16S rRNA sequence similarity), Halomonas variabilis (98.4 %), Halomonas boliviensis (98.3 %) and Halomonas sulfidaeris (97.5 %). Other closely related species were Halomonas alkaliphila (96.5 % sequence similarity), Halomonas hydrothermalis (96.3 %), Halomonas gomseomensis (96.3 %), Halomonas venusta (96.3 %) and Halomonas meridiana (96.2 %). The major fatty acids of strain BH1T were C18 : 1
ω7c (36.3 %), C16 : 0 (18.4 %) and C19 : 0 cyclo ω8c (17.9 %). The DNA G+C content was 60.0 mol% (T
m). Ubiquinone 9 (Q-9) was the major lipoquinone. The phenotypic features, fatty acid profile and DNA G+C content further supported the placement of strain BH1T in the genus Halomonas. DNA–DNA hybridization values between strain BH1T and H. neptunia CECT 5815T, H. variabilis DSM 3051T, H. boliviensis DSM 15516T and H. sulfidaeris CECT 5817T were 19, 17, 30 and 29 %, respectively, supporting the differential taxonomic status of BH1T. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain BH1T is considered to represent a novel species, for which the name Halomonas titanicae sp. nov. is proposed. The type strain is BH1T (=ATCC BAA-1257T =CECT 7585T =JCM 16411T =LMG 25388T).
Oceanobacillus locisalsi sp. nov., isolated from a marine solar saltern
Authors: Lee Soo-Young , Oh Tae-Kwang , Kim Wonyong , Yoon Jung-Hoon
Published: January 2010

A Gram-stain-variable, motile, moderately halophilic bacterial strain, CHL-21T, was isolated from a marine solar saltern and its taxonomic position was investigated using a polyphasic approach. Optimal growth of strain CHL-21T occurred at 30–37 °C, at pH 7.0–7.5 and in the presence of 5–10 % (w/v) NaCl. In phylogenetic trees based on 16S rRNA gene sequences, strain CHL-21T fell within the cluster comprising members of the genera Oceanobacillus, Ornithinibacillus and Paucisalibacillus. Strain CHL-21T exhibited 97.1–97.2 % 16S rRNA gene sequence similarity to the type strains of the two subspecies of Oceanobacillus oncorhynchi and 92.0–94.7 % 16S rRNA gene sequence similarity to the type strains of other members of the genus Oceanobacillus and members of the genera Ornithinibacillus and Paucisalibacillus. Mean DNA–DNA reassociation values between strain CHL-21T and the type strains of the two subspecies of Oceanobacillus
oncorhynchi were 19–21 %. The cell-wall peptidoglycan of strain CHL-21T was based on meso-diaminopimelic acid, MK-7 was the predominant menaquinone, and anteiso-C15 : 0 and anteiso-C17 : 0 were the major fatty acids. The DNA G+C content was 39.8 mol%. Differential phenotypic properties, including facultatively anaerobic growth and acid production from substrates, together with its phylogenetic and genetic distinctiveness, demonstrated that strain CHL-21T is distinguishable from recognized Oceanobacillus species. On the basis of data presented, strain CHL-21T represents a novel species within the genus Oceanobacillus, for which the name Oceanobacillus locisalsi sp. nov. is proposed; the type strain is CHL-21T (=KCTC 13253T =CCUG 56608T).
Fatty Acid Activation in Cyanobacteria Mediated by Acyl-Acyl Carrier Protein Synthetase Enables Fatty Acid Recycling
Authors: Kaczmarzyk Danuta , Fulda Martin
Published: January 2010

In cyanobacteria fatty acids destined for lipid synthesis can be synthesized de novo, but also exogenous free fatty acids from the culture medium can be directly incorporated into lipids. Activation of exogenous fatty acids is likely required prior to their utilization. To identify the enzymatic activity responsible for activation we cloned candidate genes from Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942 and identified the encoded proteins as acyl-acyl carrier protein synthetases (Aas). The enzymes catalyze the ATP-dependent esterification of fatty acids to the thiol of acyl carrier protein. The two protein sequences are only distantly related to known prokaryotic Aas proteins but they display strong similarity to sequences that can be found in almost all organisms that perform oxygenic photosynthesis. To investigate the biological role of Aas activity in cyanobacteria, aas knockout mutants were generated in the background of Synechocystis sp. PCC 6803 and S. elongatus PCC 7942. The mutant strains showed two phenotypes characterized by the inability to utilize exogenous fatty acids and by the secretion of endogenous fatty acids into the culture medium. The analyses of extracellular and intracellular fatty acid profiles of aas mutant strains as well as labeling experiments indicated that the detected free fatty acids are released from membrane lipids. The data suggest a considerable turnover of lipid molecules and a role for Aas activity in recycling the released fatty acids. In this model, lipid degradation represents a third supply of fatty acids for lipid synthesis in cyanobacteria.
Strategic Distribution of Protective Proteins within Bran Layers of Wheat Protects the Nutrient-Rich Endosperm
Authors: Jerkovic Ante , Kriegel Alison M. , Bradner John R. , Atwell Brian J. , Roberts Thomas H. , Willows Robert D.
Published: January 2010

Bran from bread wheat (Triticum aestivum ‘Babbler’) grain is composed of many outer layers of dead maternal tissues that overlie living aleurone cells. The dead cell layers function as a barrier resistant to degradation, whereas the aleurone layer is involved in mobilizing organic substrates in the endosperm during germination. We microdissected three defined bran fractions, outer layers (epidermis and hypodermis), intermediate fraction (cross cells, tube cells, testa, and nucellar tissue), and inner layer (aleurone cells), and used proteomics to identify their individual protein complements. All proteins of the outer layers were enzymes, whose function is to provide direct protection against pathogens or improve tissue strength. The more complex proteome of the intermediate layers suggests a greater diversity of function, including the inhibition of enzymes secreted by pathogens. The inner layer contains proteins involved in metabolism, as would be expected from live aleurone cells, but this layer also includes defense enzymes and inhibitors as well as 7S globulin (specific to this layer). Using immunofluorescence microscopy, oxalate oxidase was localized predominantly to the outer layers, xylanase inhibitor protein I to the xylan-rich nucellar layer of the intermediate fraction and pathogenesis-related protein 4 mainly to the aleurone. Activities of the water-extractable enzymes oxalate oxidase, peroxidase, and polyphenol oxidase were highest in the outer layers, whereas chitinase activity was found only in assays of whole grains. We conclude that the differential protein complements of each bran layer in wheat provide distinct lines of defense in protecting the embryo and nutrient-rich endosperm.
Arabidopsis CULLIN4-Damaged DNA Binding Protein 1 Interacts with CONSTITUTIVELY PHOTOMORPHOGENIC1-SUPPRESSOR OF PHYA Complexes to Regulate Photomorphogenesis and Flowering Time
Authors: Chen Haodong , Huang Xi , Gusmaroli Giuliana , Terzaghi William , Lau On Sun , Yanagawa Yuki , Zhang Yu , Li Jigang , Lee Jae-Hoon , Zhu Danmeng , Deng Xing Wang
Published: January 2010

CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) possesses E3 ligase activity and promotes degradation of key factors involved in the light regulation of plant development. The finding that CULLIN4 (CUL4)-Damaged DNA Binding Protein1 (DDB1) interacts with DDB1 binding WD40 (DWD) proteins to act as E3 ligases implied that CUL4-DDB1 may associate with COP1-SUPPRESSOR OF PHYA (SPA) protein complexes, since COP1 and SPAs are DWD proteins. Here, we demonstrate that CUL4-DDB1 physically associates with COP1-SPA complexes in vitro and in vivo, likely via direct interaction of DDB1 with COP1 and SPAs. The interactions between DDB1 and COP1, SPA1, and SPA3 were disrupted by mutations in the WDXR motifs of MBP-COP1, His-SPA1, and His-SPA3. CUL4 cosuppression mutants enhanced weak cop1 photomorphogenesis and flowered early under short days. Early flowering of short day–grown cul4 mutants correlated with increased FLOWERING LOCUS T transcript levels, whereas CONSTANS transcript levels were not altered. De-etiolated1 and COP1 can bind DDB1 and may work with CUL4-DDB1 in distinct complexes, but they mediate photomorphogenesis in concert. Thus, a series of CUL4-DDB1-COP1-SPA E3 ligase complexes may mediate the repression of photomorphogenesis and, possibly, of flowering time.
Auxin-Mediated Ribosomal Biogenesis Regulates Vacuolar Trafficking inArabidopsis
Authors: Rosado Abel , Sohn Eun Ju , Drakakaki Georgia , Pan Songqin , Swidergal Alexandra , Xiong Yuqing , Kang Byung-Ho , Bressan Ray A. , Raikhel Natasha V.
Published: January 2010

In plants, the mechanisms that regulate the transit of vacuolar soluble proteins containing C-terminal and N-terminal vacuolar sorting determinants (VSDs) to the vacuole are largely unknown. In a screen for Arabidopsis thaliana mutants affected in the trafficking of C-terminal VSD containing proteins, we isolated the ribosomal biogenesis mutant rpl4a characterized by its partial secretion of vacuolar targeted proteins and a plethora of developmental phenotypes derived from its aberrant auxin responses. In this study, we show that ribosomal biogenesis can be directly regulated by auxins and that the exogenous application of auxins to wild-type plants results in vacuolar trafficking defects similar to those observed in rpl4a mutants. We propose that the influence of auxin on ribosomal biogenesis acts as a regulatory mechanism for auxin-mediated developmental processes, and we demonstrate the involvement of this regulatory mechanism in the sorting of vacuolar targeted proteins in Arabidopsis.
Tomato 14-3-3 Protein 7 Positively Regulates Immunity-Associated Programmed Cell Death by Enhancing Protein Abundance and Signaling Ability of MAPKKK α
Authors: Oh Chang-Sik , Pedley Kerry F. , Martin Gregory B.
Published: January 2010

Programmed cell death (PCD) is triggered when Pto, a Ser-Thr protein kinase, recognizes either the AvrPto or AvrPtoB effector from Pseudomonas syringae pv tomato. This PCD requires mitogen-activated protein kinase kinase kinase (MAPKKK α ) as a positive regulator in tomato (Solanum lycopersicum) and Nicotiana benthamiana. To examine how PCD-eliciting activity of the tomato MAPKKK α protein is regulated, we screened for MAPKKK α -interacting proteins in tomato and identified a 14-3-3 protein, TFT7. Virus-induced gene silencing using the TFT7 gene in N. benthamiana compromised both Pto- and MAPKKK α -mediated PCD, and coexpression of TFT7 with tomato MAPKKK α enhanced MAPKKK α -mediated PCD. TFT7 was also required for PCD associated with several other disease resistance proteins and contributed to resistance against P. syringae pv tomato. Coexpression of TFT7 with MAPKKK α in vivo caused increased accumulation of the kinase and enhanced phosphorylation of two MAP kinases. TFT7 protein contains a phosphopeptide binding motif that is present in human 14-3-3 ε, and substitutions in this motif abolished interaction with MAPKKK α in vivo and also the PCD-enhancing activity of TFT7. A 14-3-3 binding motif, including a putative phosphorylated Ser-535, is present in the C-terminal region of MAPKKK α. An S535A substitution in MAPKKK α reduced interaction with TFT7 and both PCD-eliciting ability and stability of MAPKKK α. Our results provide new insights into a role for 14-3-3 proteins in regulating immunity-associated PCD pathways in plants.
A Stromal Heat Shock Protein 70 System Functions in Protein Import into Chloroplasts in the Moss Physcomitrella patens
Authors: Shi Lan-Xin , Theg Steven M.
Published: January 2010

Heat shock protein 70s (Hsp70s) are encoded by a multigene family and are located in different cellular compartments. They have broad-ranging functions, including involvement in protein trafficking, prevention of protein aggregation, and assistance in protein folding. Hsp70s work together with their cochaperones, J domain proteins and nucleotide exchange factors (e.g., GrpEs), in a functional cycle of substrate binding and release accompanied by ATP hydrolysis. We have taken advantage of the gene targeting capability of the moss Physcomitrella patens to investigate the functions of chloroplast Hsp70s. We identified four Hsp70 genes and two GrpE cochaperone homolog genes (CGE) in moss that encode chloroplast proteins. Disruption of one of the Hsp70 genes, that for Hsp70-2, caused lethality, and protein import into heat-shocked chloroplasts isolated from temperature-sensitive hsp70-2 mutants was appreciably impaired. Whereas the double cge null mutant was not viable, we recovered a cge1 null/cge2 knock down mutant in which Hsp70-2 was upregulated. Chloroplasts isolated from this mutant demonstrated a defect in protein import. In addition, two different precursors staged as early import intermediates could be immunoprecipitated with an Hsp70-2–specific antibody. This immunoprecipitate also contained Hsp93 and Tic40, indicating that it represents a precursor still in the Toc/Tic translocon. Together, these data indicate that a stromal Hsp70 system plays a crucial role in protein import into chloroplasts.
Managing quality across cultures
Authors: van den Akker Gerard J.
Published: January 2010

How does a company of 1,800 employees located at eight manufacturing sites and 15 sales offices throughout Europe overcome language barriers, national cultures and different business practices to achieve the competitive edge? The answer, according to Gerard J. van den Akker, group vice president and CEO of Avery Materials Group Europe, can be summed up in one word — Quality!
How important is it to include all epitopes in grass pollen extracts for specific immunotherapy?
Authors: Rudenko M. , Frew A. J.
Published: January 2010

Cite this as: M. Rudenko and A. J. Frew, Clinical & Experimental Allergy, 2010 (40) 365–367.
Effects of Sibship and the Presence of Multiple Predators on the Behavior of Green Frog (Rana clamitans) Tadpoles
Authors: Smith Geoffrey R. , Boyd Allison , Dayer Christopher B. , Ogle Megan E. , Terlecky Andrew J. , Dibble Christopher J.
Published: January 2010

In nature, prey are exposed to multiple predators simultaneously. We examined the effects of the cues of two potential predators, mosquitofish and odonate larvae, individually and in combination on the behavior of green frog (Rana clamitans) tadpoles. In addition to examining the behavioral response of green frog tadpoles to multiple predators, we examined variation in behavior among tadpoles from different egg masses (i.e. different sibships). Sibships differed in activity level and there was a significant predator cue by sibship interaction. Two sibships were relatively more active in the control and odonate predator cue treatments but showed reduced activity in treatments containing mosquitofish cues, whereas the remaining sibships showed consistently low levels of activity in all predator cue treatments, including the control. The use of the vegetated side of the aquarium did not differ between tadpoles exposed to the different predator cues. Sibship had no effect on tadpoles’ use of the vegetated side of the aquarium, and there was no interaction between sibship and predator cue. Our results suggest that green frogs did not respond to simultaneous exposure to multiple predator cues any differently than they did to exposure to individual predator cues. More importantly, our results suggest variation, possibly genetically based, in behavioral responses of tadpoles to predators, and thus selection on these behaviors is possible. Of particular interest is that there was variation in behavioral responses to a non‐native predator (Gambusia affinis), suggesting an evolutionary response to an invasive predator is possible.
Productive cough is an independent risk factor for the development of COPD in former smokers
Authors: YAMANE Takashi , HATTORI Noboru , KITAHARA Yoshihiro , HARUTA Yoshinori , SASAKI Hideo , YOKOYAMA Akihito , KOHNO Nobuoki
Published: January 2010

Background and objective:  It has yet to be determined whether the presence of productive cough is a risk factor for the development of COPD. The aim of the present study was to obtain more information on this potential association in Japanese men.

Methods:  Seven hundred and eighty‐three men with normal spirometry who did not have respiratory disease were recruited. The subjects were divided into three groups: group A, non‐smokers; group B, those with a positive smoking history without productive cough; and group C, those with a positive smoking history and productive cough. The incidence rates of COPD were compared among the three groups and the relative risks for the development of COPD were assessed.

Results:  During the mean follow‐up period of 33.6 ± 20.4 months, 19 (2.4%) subjects developed COPD. The incidence rate of COPD was significantly higher in group C than in group B (10.1 vs 2.2%, P = 0.003). A multivariate analysis of data for all subjects, current smokers and former smokers revealed that productive cough was an independent risk factor for the development of COPD in all subjects and former smokers but not in current smokers.

Conclusions:  Productive cough was an independent risk factor for the development of COPD in Japanese men. In particular, former smokers who complain of this symptom should be regarded as being at high risk for the development of COPD. The data suggested that stage 0 disease, as defined in the Global Initiative for Chronic Obstructive Lung Disease 2001 guidelines, is relevant for the identification of subjects at risk of developing COPD.
Reduction of rare soil microbes modifies plant–herbivore interactions
Authors: Hol W. H. Gera , De Boer Wietse , Termorshuizen Aad J. , Meyer Katrin M. , Schneider Johannes H. M. , Van Dam Nicole M. , Van Veen Johannes A. , Van Der Putten Wim H.
Published: January 2010

Ecology Letters (2010) 13: 292–301

Rare species are assumed to have little impact on community interactions and ecosystem processes. However, very few studies have actually attempted to quantify the role of rare species in ecosystems. Here we compare effects of soil community assemblages on plant‐herbivore interactions and show that reduction of rare soil microbes increases both plant biomass and plant nutritional quality. Two crop plant species growing in soil where rare microbes were reduced, had tissues of higher nutritional quality, which theoretically makes them more susceptible to pest organisms such as shoot‐feeding aphids and root‐feeding nematodes. Reduction of rare microbes increased aphid body size in the absence of nematodes; nematodes always reduced aphid body size independent of the soil microbial community. This study is the first to show that rare soil microbes are not redundant but may play a role in crop protection by enhancing aboveground and belowground plant defence. It remains to be tested whether these are direct effects of rare soil microbes on plants and herbivores, or indirect effects via shifts in the microbial soil community assemblages.
Assessment of Migraineurs Referred to a Specialist Headache Clinic in Singapore: Diagnosis, Treatment Strategies, Outcomes, Knowledge of Migraine Treatments And Satisfaction
Authors: Soon YY , Siow HC , Tan CY
Published: January 2010

This study aimed to compare (i) migraineurs' diagnosis, treatment strategies and satisfaction when treated by community care physicians (CCPs) and at the specialist headache clinic; (ii) migraineurs' knowledge of migraine treatments and outcomes at baseline and at 3 months' interval. Thirty-eight patients were interviewed at baseline visit and 3 months after neurologist consultation, using a survey form which consisted of a series of self-designed questions, the MIDAS questionnaire and the SF-36 Health Survey. More patients were informed of the diagnosis of migraine by the neurologist than by CCPs. Compared with CCPs, the neurologist was more likely to employ preventive therapies, prescribe triptans and ask patients to keep a headache diary. Patients' number of days with headaches in the last 3 months, pain intensity, MIDAS score and five out of the eight SF-36 domain scores were significantly improved at the 3 months' interval ( P < 0.05) compared with baseline at the specialist headache clinic. More patients recognized migraine-specific therapies and reported satisfaction with treatment after the neurologist consultation. This is the first study detailing significant improvements in patients' clinical outcomes, knowledge of migraine treatments and satisfaction after consultation at a specialist headache clinic in Singapore.
Detection of Gunshot Primer Residue on Bone in an Experimental Setting—An Unexpected Finding*
Authors: Berryman Hugh E. , Kutyla Alicja K. , Russell Davis J.
Published: January 2010

Abstract:  Pork ribs with intact muscle tissue were used in an experimental attempt to identify bullet wipe on bone at distances from 1 to 6 feet with 0.45 caliber, full metal jacket ammunition. This resulted in the unexpected finding of primer‐derived gunshot residue (GSR) deep within the wound tract. Of significance is the fact that the GSR was deposited on the bone, under the periosteum, after the bullet passed through a Ziploc® bag and c. 1 inch of muscle tissue. It is also important to note that the GSR persisted on the bone after the periosteum was forcibly removed. The presence of primer‐derived GSR on bone provides the potential to differentiate gunshot trauma from blunt trauma when the bone presents an atypical gunshot wound. In this study, the presence of gunshot primer residue at a distance of 6 feet demonstrates the potential for establishing maximum gun‐to‐target distance for remote shootings.
Optimal microvessel density from composite graft of autogenous maxillary cortical bone and anorganic bovine bone in sinus augmentation: influence of clinical variables
Authors: Galindo‐Moreno Pablo , Padial‐Molina Miguel , Fernández‐Barbero Juan Emilio , Mesa Francisco , Rodríguez‐Martínez Dolores , O'Valle Francisco
Published: January 2010

Objectives: The objectives of this study were to assess the microvessel density (MVD) of intra‐sinus grafts after 6 months of wound healing and to study the relationship between revascularization processes and patient clinical variables and habits.

Material and methods: We performed 45 maxillary sinus augmentations with different implant placements in 25 consecutive patients, obtaining bone cores of the grafted area for histological, histomorphometric and immunohistochemical study. Biopsies were also taken from pristine bone in the posterior maxilla (control).

Results: All implants survived at 24 months. Biopsies of sinus augmentation areas showed significantly greater remodeling activity vs. pristine bone, with significantly more osteoid lines. The morphometry study revealed 34.88±15.2% vital bone, 32.02±15.1% non‐mineralized tissue and 33.08±25.4% remnant anorganic bovine bone particles. The number of CD34‐positive vessels was 86.28±55.52/mm2 in graft tissue vs. 31.52±13.69/mm2 in native tissue (P=0.002, Mann–Whitney U=46). The larger amount of non‐mineralized tissue in grafts was directly correlated with a higher MVD (r=0.482, P=0.0001, Pearson's test). MVD was affected by the presence of periodontitis or tobacco and alcohol consumption.

Conclusion: The angiogenesis and revascularization obtained by this type of graft achieve adequate tissue remodeling for osseointegration and are influenced by periodontal disease and tobacco or alcohol consumption.

To cite this article:
 Galindo‐Moreno P, Padial‐Molina M, Fernández‐Barbero JE, Mesa F, Rodríguez‐Martínez D, O'Valle F. Optimal microvessel density from composite graft of autogenous maxillary cortical bone and anorganic bovine bone in sinus augmentation: influence of clinical variables. Clin. Oral Impl. Res. 21, 2010; 221–227 doi: 10.1111/j.1600‐0501.2009.01827.x
The role of successional stage and small‐scale disturbance for establishment of pioneer grass Corynephorus canescens
Authors: Tschöpe Okka , Tielbörger Katja
Published: January 2010

Question: Which mechanisms promote the maintenance of the protected pioneer grass Corynephorus canescens in a mosaic landscape? Which are the interactive effects of small‐scale disturbances, successional stage and year‐to‐year variation on early establishment probabilities of C. canescens?

Location: Brandenburg, NE Germany.

Methods: We measured emergence and survival rates over 3 yr in a sowing‐experiment conducted in three successional stages (C. canescens‐dominated site, ruderal forb site and pioneer forest) under two different regimes of mechanical ground disturbance (disturbed versus undisturbed control).

Results: Overall, disturbance led to higher emergence in a humid year and to lower emergence in a very dry year. Apparently, when soil moisture was sufficient, the main factor limiting C. canescens' establishment was competition, while in the dry year, water became the limiting factor. Survival rates were not affected by disturbance. In humid years, C. canescens emerged in higher numbers in open successional stages while in the dry year, emergence rates were higher in late stages, suggesting an important role of late successional stages for the persistence of C. canescens.

Conclusions: Our results suggest that small‐scale disturbances can promote germination of C. canescens. However, disturbances should be carefully planned. The optimal strategy for promoting C. canescens is to apply disturbances just before seed dispersal and not during dry years. At the landscape scale, a mosaic of different vegetation types is beneficial for the protected pioneer grass as facilitation by late‐successional species may be an important mechanism for the persistence of C. canescens, especially in dry years.
Viroids: Small Probes for Exploring the Vast Universe of RNA Trafficking in Plants
Authors: Wang Ying , Ding Biao
Published: January 2010

Cell‐to‐cell and long‐distance trafficking of RNA is a rapidly evolving frontier of integrative plant biology that broadly impacts studies on plant growth and development, spread of infectious agents and plant defense responses. The fundamental questions being pursued at the forefronts revolve around function, mechanism and evolution. In the present review, we will first use specific examples to illustrate the biological importance of cell‐to‐cell and long‐distance trafficking of RNA. We then focus our discussion on research findings obtained using viroids that have advanced our understanding of the underlying mechanisms involved in RNA trafficking. We further use viroid examples to illustrate the great diversity of trafficking machinery evolved by plants, as well as the promise for new insights in the years ahead. Finally, we discuss the prospect of integrating findings from different experimental systems to achieve a systems‐based understanding of RNA trafficking function, mechanism and evolution.
Transcriptional Regulation of Secondary Growth and Wood Formation
Authors: Du Juan , Groover Andrew
Published: January 2010

Secondary growth and wood formation are products of the vascular cambium, a lateral meristem. Although the mechanisms have only recently begun to be uncovered, transcriptional regulation appears increasingly central to the regulation of secondary growth. The importance of transcriptional regulation is illustrated by the correlation of expression of specific classes of genes with related biological processes occurring at specific stages of secondary growth, including cell division, cell expansion, and cell differentiation. At the same time, transcription factors have been characterized that affect specific aspects of secondary growth, including regulation of the cambium and differentiation of cambial daughter cells. In the present review, we summarize evidence pointing to transcription as a major mechanism for regulation of secondary growth, and outline future approaches for comprehensively describing transcriptional networks underlying secondary growth.
Self-consistent analysis of OH Zeeman observations
Authors: Crutcher Richard M. , Hakobian Nicholas , Troland Thomas H.
Published: January 2010

Crutcher et al. used OH Zeeman observations of four nearby molecular dark clouds to show that the ratio of mass to magnetic flux was smaller in the ∼0.1 pc cores than in the ∼1 pc envelopes, in contradiction to the prediction of ambipolar diffusion driven core formation. A crucial assumption was that the magnetic field direction is nearly the same in the envelope and core regions of each cloud. Mouschovias & Tassis have argued that the data are not consistent with this assumption, and presented a new analysis that changes the conclusions of the study. Here, we show that the data are in fact consistent with the nearly uniform field direction assumption; hence, the original study is internally self-consistent and the conclusions are valid under the assumptions that were made. We also show that the Mouschovias & Tassis model of magnetic fields in cloud envelopes is inconsistent with their own analysis of the data. However, the data do not rule out a more complex field configuration that future observations may discern.
Mapping Social Capital: A Critical Contextual Approach For Working With Low‐Status Families
Authors: Garcia Marisol , McDowell Teresa
Published: January 2010

Promoting justice in therapeutic work with families demands an analysis of contextual factors such as race, ethnicity, gender, and social class in relationship to societal systems of power, privilege, and oppression. A broad understanding of these dynamics, however, is inadequate to inform our work with families whose social capital severely limits available life choices, social influence, and material resources. In this article, we describe working from a critical contextual perspective to consider how families gain and/or lose social capital through participation in multiple contexts. We introduce a technique for mapping social capitol within and across multiple systems as well as suggestions for interventions aimed at increasing the social well‐being of low‐status families. These include considering the dynamics of boundary crossing, recognizing and optimizing resistance to oppressive dynamics, finding ways to limit constraints and optimize opportunities, and developing webs of allies to support family functioning and access to resources. We offer the example of 13‐year‐old Pepe as a case in point.
The Extracellular Signal‐Regulated Kinase Is Involved in the Effects of Sildenafil on Pulmonary Vascular Remodeling
Authors: Zeng Zhen , Li Yingchuan , Jiang Zhen , Wang Chunsheng , Li BingBing , Jiang Wei
Published: January 2010

Pulmonary hypertension is a group of diseases comprising vascular constriction and obstructive changes of the pulmonary vasculature. Phosphodiesterase type 5 inhibitors, for example, sildenafil, can alleviate vascular remodeling in the monocrotaline pulmonary hypertension model in rats. We investigate the mechanisms of sildenafil on the pulmonary vascular remodeling of pulmonary hypertension induced by monocrotaline (MCT) in rats. Thirty Sprague‐Dawley rats (weighing 200–220 g) were administered with MCT abdominal cavity injection or equivalent volume of normal saline (NS) (which were treated as C group n = 10) to induce pulmonary hypertension model. Fourteen days later, 20 MCT treated rats were randomly fed with sildenafil (25mg/kg/day) or placebo as S, P group (10 rats for each group), respectively. Another 6 weeks later, mean pulmonary artery pressure (mPAP), index of right ventricular hypertrophy (RV/LV+S) of all animals were measured under general anesthesia. Pulmonary tissue was collected to investigate pathological features of pulmonary arteries and to measure protein expression of ERK1/ERK2 and MKP1. After 6 weeks, there were significant elevated mPAP and RV/LV+S in both P and S groups. The ratio of wall thickness to vessel diameter in pulmonary arteries with diameters <200 μm were increased in both P and S groups. But the ratio of wall thickness to vessel diameter was smaller in S group than that in P group. The phosphorylation level of ERK1/ERK2 were elevated in both P and S groups, but the level of phosphorlation ERK1/ERK2 were lower in S group than that in P group. Intriguingly, the expression level of MKP1 was significantly increased in both S and P groups, while it was higher in S group than that in P group. The Sildenafil can decrease mPAP and inhibit the progress of pulmonary vascular remodeling in pulmonary hypertension rats. The ERK‐MAP kinase signaling pathway might play a role during this process.
Over‐expression of Toll‐like receptors and their ligands in small‐for‐size graft
Authors: Jiang Weiwei , Hu Mingzheng , Rao Jianhua , Xu Xiaoqun , Wang Xuehao , Kong Lianbao
Published: January 2010

Aim:  Toll‐like receptors (TLRs) participate in several physiological and pathological processes of transplantation, including inflammation and allograft rejection, but the expression of TLRs and their ligands remains undetermined in small‐for‐size graft transplantation.

Methods:  A non‐arterialized partial liver transplantation model was used. The expression of TLR2 and TLR4 mRNA and protein, CD14 and Myeloid Differentiation‐2 (MD‐2) mRNA, as well as TLR2 and TLR4 exogenous ligands (endotoxin) and endogenous ligands [heat shock protein (HSP) 60 and 70] were assessed. The signaling pathways induced by TLR2 and TLR4 were also assessed.

Results:  In small‐for‐size liver graft, the expression of mRNA and protein of TLR2 and TLR4, CD14 and MD‐2 mRNA, as well as endogenous ligands of TLR2 and TLR4 such as HSP60 and HSP70 was quickly and significantly increased after reperfusion, and reached a peak at 3 h after reperfusion. The levels of exogenous ligands (endotoxin) were increased and reached a peak at 6 h after reperfusion. The appearance of TLR2 and TLR4 mRNA was accompanied by increased HSP 60 and 70 mRNA within 24 h after reperfusion. In the small‐for‐size group, the peak levels of TLRs and their endogenous ligands appeared earlier than those in the full size group; the peak levels of TLRs and their endogenous and exogenous ligands were higher than those in the full size group.

Conclusion:  TLR2 and TLR4, as well as their endogenous and exogenous ligands were activated in small‐for‐size liver graft transplantation.
Sympathetic and haemodynamic responses to lipids in healthy human ageing
Authors: Florian John P. , Pawelczyk James A.
Published: January 2010

Plasma non‐esterified fatty acids (NEFAs) activate the sympathetic nervous system and increase vascular resistance and blood pressure (BP); however, the response with ageing is not known. The objectives of this study were to characterize the cardiovascular, neural and endocrine responses to acute elevation of NEFA concentration. Seventeen healthy older volunteers (7 male and 10 female; age, 69 ± 1 years; body mass index, 24 ± 0 kg m−2; values are means ±s.e.m.) received a 4 h intravenous infusion of the lipid emulsion Intralipid® 20% or placebo (single‐blind, randomized, balanced order) on two different days separated by at least 2 weeks. Muscle sympathetic nerve activity (MSNA), heart rate (HR), BP, cardiac output, leptin, insulin, aldosterone, angiotensin II and F2‐isoprostanes were measured. The change in HR (+8.8 ± 0.9 versus+3.0 ± 0.9 beats min−1), systolic BP (+13.9 ± 2.2 versus+6.6 ± 2.4 mmHg) and diastolic BP (+7.4 ± 1.5 versus+1.3 ± 0.8 mmHg) was significantly greater after Intralipid®versus placebo infusions (P < 0.001). Lipid infusion increased MSNA burst frequency (+6.7 ± 1.6 bursts min−1), total MSNA (+45%; P < 0.001) and concentrations of insulin (+40%), aldosterone (+50%) and F2‐isoprostanes (+80%), but not leptin. Hyperlipidaemia caused directionally opposite responses for insulin (increased) and calf vascular resistance (decreased) in men, whereas insulin and calf vascular resistance responses were severely blunted and non‐existent, respectively, in women. We conclude that direct vascular mechanisms and central sympathetic activation contribute to the NEFA pressor response; though absolute values are higher, the change is not different compared with previous studies in a younger population.