bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel role of CD1c in regulating CD1d-mediated NKT cell recognition by competitive binding to Ig-like transcript 4
Authors: Li Demin , Hong An , Lu Qiong , Gao George F. , Jin Boquan , Screaton Gavin R. , Xu Xiao-Ning
Published: August 2012

Humans express four MHC-like CD1 molecules CD1a, b, c and d that are capable of presenting a wide variety of self or foreign lipid antigens to T cells. Much progress has been made in elucidating the function of CD1d-restricted NKT cells in both innate and adaptive immune responses. However, knowledge of the other CD1 molecules is less well defined in terms of lipid presentation and immune regulation. We have previously shown that immunoglobulin-like transcript 4 (ILT4) binds to CD1d and inhibits its recognition by NKT cells. In this study, we show that CD1c can also interact specifically with ILT4 with a higher affinity than that of CD1d. Furthermore, changes in CD1c expression seem to modulate CD1d function; up-regulation of CD1c enhances NKT recognition of CD1d and down-regulation reduces CD1d recognition. We propose that CD1c can act as a sink for the inhibitory receptor ILT4: when CD1c is up-regulated, ILT4 is recruited to CD1c, thus reducing the inhibitory effect of ILT4 on CD1d recognition. Consequently, CD1c could be a potential target for modulating NKT activity.Keywords: NKT, CD1d, CD1c, ILT4, antigen presentation
Decoherence in the chemical compass: the role of decoherence for avian magnetoreception
Authors: Tiersch Markus , Briegel Hans J.
Published: August 2012

Contrary to the usual picture that decoherence destroys quantum properties and causes the quantum-to-classical transition, we argue that decoherence can also play a constructive role in driving quantum dynamics and amplifying its results to macroscopic scales. We support this perspective by presenting an example system from spin chemistry, which is also of importance for biological systems, e.g. in avian magnetoreception.
Temperature of a decoherent oscillator with strong coupling
Authors: Unruh W. G.
Published: August 2012

The temperature of an oscillator coupled to the vacuum state of a heat bath via Ohmic coupling is non-zero, as measured by the reduced density matrix of the oscillator. This study shows that the actual temperature, as measured by a thermometer, is still zero (or, in the thermal state of the bath, the temperature of the bath). The decoherence temperature is due to ‘false-decoherence’, with a correlation between the oscillator and the heat bath causing the decoherence, but the heat baths state dragged along with the state of the oscillator.
Decoherence without dissipation
Authors: Unruh W. G.
Published: August 2012

That decoherence can take place in the presence of energy conservation seems to be a poorly known fact. That lack of knowledge has, for example, bedevilled the discussion of the ‘black hole information’ problem. I present a simple model that illustrates such energy-free decoherence.
Ornithinimicrobium murale sp. nov., isolated from an indoor wall colonized by moulds
Authors: Kämpfer P. , Glaeser S. P. , Schäfer J. , Lodders N. , Martin K. , Schumann P.
Published: August 2012

A Gram-positive, non-spore-forming actinobacterium (01-Gi-040T) isolated from an indoor wall was studied to examine its taxonomic position. The isolate formed a very rudimentary substrate-mycelium that fragmented into rod-shaped to coccoid cells. On the basis of the 16S rRNA gene sequence similarity studies, strain 01-Gi-040T was shown to belong to the genus

Ornithinimicrobium

closely related to

Ornithinimicrobium kibberense

K22-20T (97.1 %),

Ornithinimicrobium humiphilum

DSM 12362T (96.2 %) and

Ornithinimicrobium pekingense

LW6T (96.1 %). A close relationship was also found with

Arsenicicoccus bolidensis

CCUG 47306T (95.9 %) and

Arsenicicoccus piscis

Kis4-19T (95.7 %) and a moderate relationship to the type strains of the genus

Serinicoccus

(94.0–94.1 %). The predominant menaquinone of strain 01-Gi-040T was MK-8(H4). The peptidoglycan contained ornithine as the diagnostic diamino acid. The polar lipid profile consisted of the lipids phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid, an unknown aminolipid and two unknown phosphoglycolipids. The major fatty acids iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 were consistent with the fatty acid patterns reported for members of the genus

Ornithinimicrobium

. The results of DNA–DNA hybridizations, physiological and biochemical tests allowed phenotypic differentiation of strain 01-Gi-040T from the three recognized species of the genus

Ornithinimicrobium

. Strain 01-Gi-040T represents a novel species of the genus

Ornithinimicrobium

, for which we propose the name Ornithinimicrobium murale sp. nov., with the type strain 01-Gi-040T ( = DSM 22056T = CCM 7610T).
Lysinibacillus meyeri sp. nov., isolated from a medical practice
Authors: Seiler Herbert , Scherer Siegfried , Wenning Mareike
Published: August 2012

A Gram-positive, oxidase- and catalase-positive, strictly aerobic and motile bacterium, designated WS 4626T, was isolated from a medical practice. Spherical endospores were formed terminally in swollen rods. The genomic DNA G+C content was 37.1 mol%. Cells contained iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω10c, anteiso-C17 : 0 and iso-C17 : 0 as the predominant cellular fatty acids and MK-7 and MK-6 as the major isoprenoid quinones. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, the cell-wall peptidoglycan was type A4α, l-Lys-d-Asp and the major cell-wall sugar was xylose. The closest phylogenetic relatives were

Lysinibacillus xylanilyticus

XDB9T (96.7 % 16S rRNA gene sequence similarity) and

Lysinibacillus odysseyi

34hs-1T (96.5 %). DNA–DNA relatedness between the isolate and

L. odysseyi

DSM 18869T was very low (6 %). On the basis of the data presented, strain WS 4626T represents a novel species of the genus

Lysinibacillus

, for which the name Lysinibacillus meyeri sp. nov. is proposed. The type strain is WS 4626T ( = DSM 25057T = LMG 26643T).
Iodobacter limnosediminis sp. nov., isolated from Arctic lake sediment
Authors: Su Wei , Zhou Zhichao , Jiang Fan , Chang XuLu , Liu Ying , Wang Shaohua , Kan Wenjing , Xiao Mengchen , Shao Ming , Peng Fang , Fang Chengxiang
Published: August 2012

A Gram-reaction-negative, motile, non-violet-pigmented, rod-shaped bacterial strain, designated E1T, was isolated from Arctic lake sediment. Growth occurred at 4 °C–28 °C (optimum, 18 °C), at pH 4–11(optimum, 9–10) and in the presence of 0–1 % (w/v) NaCl. The taxonomic position of E1T was analysed using a polyphasic approach. Strain E1T exhibited 16S rRNA gene sequence similarity value of 98.1 % with respect to the type strain of

Iodobacter fluviatilis

, but no more than 93 % with the type strains of other recognized species. A further DNA–DNA hybridization experiment was conducted, which demonstrated unambiguously that strain E1T was distinct from

I. fluviatilis

ATCC 33051T (51.3 % relatedness). The DNA G+C content of strain E1T was 52.3 mol%. Chemotaxonomic data [Q-8 as the monospecific respiratory quinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 56.1 %) and C16 : 0 (18.8 %) as the major cellular fatty acids] supported the affiliation of strain E1T to the genus

Iodobacter

. However, the results of physiological and biochemical tests allowed phenotypic differentiation of strain E1T from

I. fluviatilis

ATCC 33051T. On the basis of phenotypic and genotypic properties, strain E1T represents a novel species of genus Iodobacter, for which the name Iodobacter limnosediminis sp. nov. is proposed. The type strain is E1T ( = CCTCC AB 2010224T = NRRL B-59456T).
Dokdonella kunshanensis sp. nov., isolated from activated sludge, and emended description of the genus

Dokdonella
Authors: Li Yi , Zhang Jun , Chen Qing , Yang Guiqin , Cai Shu , He Jian , Zhou Shungui , Li Shun-Peng
Published: August 2012

A Gram-negative, aerobic, non-motile, non-spore-forming rod, designated DC-3T, was isolated from activated sludge of a wastewater treatment plant in China. Comparative 16S rRNA gene sequence analysis showed that strain DC-3T belonged to the family

Xanthomonadaceae

and formed a lineage within the genus

Dokdonella

. Strain DC-3T shared the highest 16S rRNA gene sequence similarity with

Dokdonella soli

KIS28-6T (97.1 %) and

Dokdonella fugitiva

A3T (97.1 %). The G+C content of the genomic DNA was 71.5 mol%. The major respiratory quinone was Q-8 and the major fatty acids were iso-C17 : 1ω9c (31.6 %), iso-C15 : 0 (12.6 %), iso-C16 : 0 (21.3 %), iso-C17 : 0 (13.1 %) and iso-C11 : 0 3-OH (6.5 %), which supported the affiliation of strain DC-3T with the genus

Dokdonella

. DNA–DNA relatedness between strain DC-3T and its closest phylogenetic neighbours was <30 %. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain DC-3T from the recognized species of the genus

Dokdonella

. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DC-3T represents a novel species of the genus

Dokdonella

, for which the name Dokdonella kunshanensis sp. nov. is proposed. The type strain is DC-3T ( = CCTCC AB 2011179T  = KACC 16511T). The description of the genus

Dokdonella

is also emended.
Dokdonella immobilis sp. nov., isolated from a batch reactor for the treatment of triphenylmethane dye effluent
Authors: Liu Ying , Jin Jing-Hua , Liu Hong-Can , Liu Zhi-Pei
Published: August 2012

A Gram-staining-negative, non-endospore-forming, non-flagellated, non-motile and rod-shaped bacterium, designated strain LM2-5T, was isolated from activated sludge in a sequencing batch reactor used for the treatment of triphenylmethane dye effluent. The taxonomy of strain LM2-5T was studied by phenotypic, chemotaxonomic and phylogenetic methods. Strain LM2-5T was aerobic, heterotrophic and positive for oxidase but negative for catalase activity. It grew at 16–37 °C (optimum 25 °C) and at pH 5.0–8.5 (optimum between pH 6.5 and pH 7.0). NaCl was not obligatory for growth but was tolerated at concentrations up to 2.0 % (w/v) NaCl. The novel strain formed yellow colonies on trypticase soy agar. Cells of strain LM2-5T were rods that measured 0.3–0.5 µm in width and 3.0–5.0 µm in length. The predominant respiratory quinone was Q-8. The major fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c. The genomic DNA G+C content was 66.7 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, strain LM2-5T clustered with members of the genus

Dokdonella

and appeared most closely related to

Dokdonella koreensis

DS-123T (96.4 % sequence similarity),

Dokdonella fugitiva

A3T (96.1 %),

Dokdonella soli

KIS28-6T (95.7 %) and

Dokdonella ginsengisoli

Gsoil 191T (95.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain LM2-5T was considered to represent a novel species of the genus

Dokdonella

, for which the name Dokdonella immobilis is proposed. The type strain is LM2-5T ( = CGMCC 1.7659T  = JCM 15763T).
Marinivirga aestuarii gen. nov., sp. nov., a member of the family

Flavobacteriaceae

, isolated from marine environments, and emended descriptions of the genera

Hyunsoonleella

,

Jejuia

and

Pontirhabdus

and the species

Hyunsoonleella jejuensis

,

Jejuia pallidilutea

and

Pontirhabdus pectinivorans
Authors: Park Seong Chan , Choe Han Na , Hwang Yeoung Min , Baik Keun Sik , Kim Se Na , Lee Young Sun , Jung Jae Sung , Seong Chi Nam
Published: August 2012

Two orange, rod-shaped, Gram-reaction-negative, aerobic bacterial strains devoid of flagella and gliding motility, designated strains KYW371T and KS18 were isolated from a seawater sample and a shellfish Ruditapes philippinarum, respectively, collected from Gwangyang Bay, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the family

Flavobacteriaceae

; and that strain KYW371T was most closely related to

Algibacter mikhailovii

LMG 23988T (96.7 % sequence similarity),

Pontirhabdus pectinivorans

JC2675T (96.3 %),

Postechiella marina

M091T (95.6 %) and

Hyunsoonleella jejuensis

CNU004T (95.3 %). The 16S rRNA gene sequence similarity (98.8 %) and DNA–DNA relatedness (78.1 %) between strains KYW371T and KS18 indicated that these two strains represented a single species. The predominant cellular fatty acids of strain KYW371T were iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. Flexirubin-type pigments were absent. MK-6 was the only isoprenoid quinone and the DNA G+C content was 34.8–36.6 mol%. Data from this taxonomic study employing a polyphasic approach suggested that the isolates represent a novel species in a new genus in the family

Flavobacteriaceae

, for which the name Marinivirga aestuarii gen. nov., sp. nov. is proposed. The type strain is KYW371T ( = KCTC 23449T = JCM 17452T), and an additional strain of the species is KS18 ( = KCTC 23128 = JCM 16845). Emended descriptions of the genera

Hyunsoonleella

,

Jejuia

and

Pontirhabdus

and the species

Hyunsoonleella jejuensis

,

Jejuia pallidilutea

and

Pontirhabdus pectinivorans

are also proposed.
Streptomyces ziwulingensis sp. nov., isolated from grassland soil
Authors: Lin Yan Bing , Wang Xin Ye , Wang Ting Ting , An Shao Shan , Shi Peng , Wei Ge Hong
Published: August 2012

A novel actinobacterium, designated strain F22T, was isolated from grassland soil collected from the Ziwuling area on the Loess Plateau, China. The novel strain was found to have morphological and chemotaxonomic characteristics typical of members of the genus

Streptomyces

. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain F22T belonged to the genus

Streptomyces

, being most closely related to

Streptomyces resistomycificus

NBRC 12814T (98.28 % sequence similarity),

Streptomyces ciscaucasicus

NBRC 12872T (98.14 %),

Streptomyces chartreusis

NBRC 12753T (98.14 %) and

Streptomyces canus

NRRL B-1989T (98.14 %). In DNA–DNA hybridizations and comparisons of morphological and phenotypic data, strain F22T could be distinguished from all of its closest phylogenetic relatives. Strain F22T exhibited antibacterial and antifungal activity, especially against

Staphylococcus aureus

,

Bacillus subtilis

and Cylindrocarpon destructans. Based on the DNA–DNA hybridization data and morphological, phenotypic and phylogenetic evidence, strain F22T represents a novel species of the genus

Streptomyces

, for which the name Streptomyces ziwulingensis sp. nov. is proposed. The type strain is F22T ( = CCNWFX 0001T = JCM 18081T = ACCC41875T).
Gemmobacter tilapiae sp. nov., a poly-β-hydroxybutyrate-accumulating bacterium isolated from a freshwater pond
Authors: Sheu Shih-Yi , Sheu Der-Shyan , Sheu Fu-Sian , Chen Wen-Ming
Published: August 2012

A novel bacterium, designated strain Ruye-53T, was isolated from a freshwater pond used to rear tilapiine cichlid fish in Taiwan. The taxonomic position of the novel strain was determined using a polyphasic approach. Strain Ruye-53T was Gram-reaction-negative, aerobic, cream–white coloured, rod-shaped, non-motile and poly-β-hydroxybutyrate-accumulating. Growth occurred at 10–37 °C (optimum between 20 and 25 °C), at pH 6.0–9.0 (optimum between pH 8.0 and pH 9.0) and with 0–1 % (w/v) NaCl (optimum 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Ruye-53T belonged to the genus

Gemmobacter

and that its most closely related neighbour was

Gemmobacter aquatilis

DSM 3857T (97.6 % sequence similarity). The novel strain’s predominant fatty acid was C18 : 1ω7c, its major respiratory quinone was Q-10 and its genomic DNA G+C content was 61.2 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one uncharacterized aminolipid and four uncharacterized phospholipids. The DNA–DNA relatedness value between strain Ruye-53T and

Gemmobacter aquatilis

DSM 3857T was about 45.5 % (48.2±0.4 % in the reciprocal experiment). On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Ruye-53T represents a novel species in the genus

Gemmobacter

, for which the name Gemmobacter tilapiae sp. nov. is proposed. The type strain is Ruye-53T ( = BCRC 80261T  = KCTC 23310T).
Pichia bruneiensis sp. nov., a biofilm-producing dimorphic yeast species isolated from flowers in Borneo
Authors: Sipiczki Matthias
Published: August 2012

Taxonomic analysis of five yeast strains isolated from Hibiscus flowers in Brunei (Borneo) is described. The strains represent a dimorphic, biofilm-producing, anamorphic budding yeast species for which the name Pichia bruneiensis is proposed. P. bruneiensis alternates between yeast and pseudohyphal modes of growth. The pseudohyphae form biofilms on the surface of liquid media and penetrate into solid substrates. The sequences of the D1/D2 domains of the large subunit rRNA genes, the internal transcribed spacer (ITS) regions and the 18S rRNA genes were identical in the five strains and indicated a close phylogenetic relationship with teleomorph species of the genus Pichia. In a phylogenetic analysis of these sequences, the closest relative of the new species was Pichia fermentans (6 % nucleotide substitutions and indels in the D1/D2 domain). The type strain is 11-485T and has been deposited in the Centralbureau voor Schimmelcultures (Utrecht, the Netherlands) as CBS 12611T, the National Collection of Agricultural and Industrial Micro-organisms (Budapest, Hungary) as NCAIM Y.02019T and the Culture Collection of Yeasts (Bratislava, Slovakia) as CCY 29-189-1T. Mycobank no. MB800537.
Dehalogenimonas alkenigignens sp. nov., a chlorinated-alkane-dehalogenating bacterium isolated from groundwater
Authors: Bowman Kimberly S. , Nobre M. Fernanda , da Costa Milton S. , Rainey Fred A. , Moe William M.
Published: August 2012

Two strictly anaerobic bacterial strains, designated IP3-3T and SBP-1, were isolated from groundwater contaminated by chlorinated alkanes and alkenes at a Superfund Site located near Baton Rouge, Louisiana (USA). Both strains reductively dehalogenate a variety of polychlorinated aliphatic alkanes, including 1,2-dichloroethane, 1,2-dichloropropane, 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane and 1,2,3-trichloropropane, when provided with hydrogen as the electron donor. To clarify their taxonomic position, strains IP3-3T and SBP-1 were characterized using a polyphasic approach. Both IP3-3T and SBP-1 are mesophilic, non-spore-forming, non-motile and Gram-stain-negative. Cells of both strains are irregular cocci with diameters of 0.4–1.1 µm. Both are resistant to ampicillin and vancomycin. The genomic DNA G+C contents of strains IP3-3T and SBP-1 are 55.5±0.4 and 56.2±0.2 mol% (HPLC), respectively. Major cellular fatty acids include C18 : 1ω9c, C16 : 0, C14 : 0 and C16 : 1ω9c. 16S rRNA gene sequence based phylogenetic analyses indicated that the strains cluster within the phylum

Chloroflexi

most closely related to but distinct from the species

Dehalogenimonas lykanthroporepellens

(96.2 % pairwise similarity) and

Dehalococcoides mccartyi

(90.6 % pairwise similarity). Physiological and chemotaxonomic traits as well as phylogenetic analysis support the conclusion that these strains represent a novel species within the genus

Dehalogenimonas

for which the name Dehalogenimonas alkenigignens sp. nov. is proposed. The type strain is IP3-3T ( = JCM 17062T = NRRL B-59545T).
Azorhizobium oxalatiphilum sp. nov., and emended description of the genus

Azorhizobium
Authors: Lang Elke , Schumann Peter , Adler Susann , Spröer Cathrin , Sahin Nurettin
Published: August 2012

A Gram-negative, motile, non-spore-forming rod, designated NS12T, was isolated from macerated petioles of Rumex sp. after enrichment with oxalate. On the basis of 16S rRNA gene sequence similarity, strain NS12T was phylogenetically related to the genera

Azorhizobium

and

Xanthobacter

in the class

Alphaproteobacteria

. Strain NS12T was most closely related to

Azorhizobium doebereinerae

BR 5401T and

Azorhizobium caulinodans

ORS 571T (98.3 and 97.3 % 16S rRNA gene sequence similarity, respectively). Membership of the genus

Xanthobacter

was excluded by phenotypic characterization. The whole-cell fatty acid compositions of the isolate was typical of members of the genus

Azorhizobium

with C18 : 1ω7c, cyclo-C19 : 0ω8c, 11-methyl-C18 : 1ω7c and C16 : 0 as the main components. The results of DNA–DNA hybridization and physiological tests allowed the genotypic and phenotypic differentiation of strain NS12T from the two members of the genus

Azorhizobium

. Therefore it is concluded that the isolate represents a novel species of the genus

Azorhizobium

, for which the name Azorhizobium oxalatiphilum sp. nov. is proposed. The type strain is NS12T ( = DSM 18749T = CCM 7897T). The description of the genus

Azorhizobium

is also emended.
Lentisphaera marina sp. nov., and emended description of the genus

Lentisphaera
Authors: Choi Ahyoung , Yang Seung-Jo , Rhee Kwang-Hyun , Cho Jang-Cheon
Published: August 2012

Two Gram-stain-negative, non-motile, non-pigmented cocci, designated IMCC11369T and IMCC11389, were isolated from surface seawater of the East Sea of Korea by high-throughput cultivation based on dilution to extinction. Strains IMCC11369T and IMCC11389 shared 99.9 % 16S rRNA gene sequence similarity and >86.3 % DNA–DNA relatedness, which suggested that they belong to the same genomic species. The isolates were most closely related to

Lentisphaera araneosa

HTCC2155T (99.0 % 16S rRNA gene sequence similarity). Phylogenetic analysis revealed that the isolates formed a robust cluster with

L. araneosa

HTCC2155T. DNA–DNA relatedness values, however, showed that the isolates were distantly related to

L. araneosa

HTCC2155T (2.0–18.6 %), which suggested that they represent a separate genomic species in the genus

Lentisphaera

. The two isolates were phenotypically differentiated from their closest relative by several characteristics, including degradation of macromolecules and carbon source utilization. The DNA G+C content was 44.5–45.2 mol% and the predominant cellular fatty acids were C14 : 0, C16 : 1ω9c and C16 : 0. Strain IMCC11369T contained MK-7 as the respiratory quinone and phosphatidylethanolamine and an unknown lipid as the major polar lipids. On the basis of data obtained in this study, a novel species is proposed to accommodate the isolates, Lentisphaera marina sp. nov. The type strain is IMCC11369T ( = KCTC 23780T = NBRC 108776T).
Copy-number-aware differential analysis of quantitative DNA sequencing data
Authors: Robinson Mark D. , Strbenac Dario , Stirzaker Clare , Statham Aaron L. , Song Jenny , Speed Terence P. , Clark Susan J.
Published: August 2012

Developments in microarray and high-throughput sequencing (HTS) technologies have resulted in a rapid expansion of research into epigenomic changes that occur in normal development and in the progression of disease, such as cancer. Not surprisingly, copy number variation (CNV) has a direct effect on HTS read densities and can therefore bias differential detection results. We have developed a flexible approach called ABCD-DNA (affinity-based copy-number-aware differential quantitative DNA sequencing analyses) that integrates CNV and other systematic factors directly into the differential enrichment engine.
Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
Authors: Fritsch Claudia , Herrmann Alexander , Nothnagel Michael , Szafranski Karol , Huse Klaus , Schumann Frank , Schreiber Stefan , Platzer Matthias , Krawczak Michael , Hampe Jochen , Brosch Mario
Published: August 2012

So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells to generate a transcriptome-wide map of TISs in a human monocytic cell line. A neural network was trained on the ribosomal footprints observed at previously annotated AUG translation initiation codons (TICs), and used for the ab initio prediction of TISs in 5062 transcripts with sufficient sequence coverage. Functional interpretation suggested 2994 novel upstream open reading frames (uORFs) in the 5′ UTR, 1406 uORFs overlapping with the coding sequence, and 546 N-terminal protein extensions. The TIS detection method was validated on the basis of previously published alternative TISs and uORFs. Among primates, TICs in newly annotated TISs were significantly more conserved than control codons, both for AUGs and near-cognate codons. The transcriptome-wide map of novel candidate TISs derived as part of the study will shed further light on the way in which human proteome diversity is influenced by alternative translation initiation and regulation.
SNF1-Related Protein Kinases Type 2 Are Involved in Plant Responses to Cadmium Stress
Authors: Kulik Anna , Anielska-Mazur Anna , Bucholc Maria , Koen Emmanuel , Szymańska Katarzyna , Żmieńko Agnieszka , Krzywińska Ewa , Wawer Izabela , McLoughlin Fionn , Ruszkowski Dariusz , Figlerowicz Marek , Testerink Christa , Skłodowska Aleksandra , Wendehenne David , Dobrowolska Grażyna
Published: August 2012

Cadmium ions are notorious environmental pollutants. To adapt to cadmium-induced deleterious effects plants have developed sophisticated defense mechanisms. However, the signaling pathways underlying the plant response to cadmium are still elusive. Our data demonstrate that SnRK2s (for SNF1-related protein kinase2) are transiently activated during cadmium exposure and are involved in the regulation of plant response to this stress. Analysis of tobacco (Nicotiana tabacum) Osmotic Stress-Activated Protein Kinase activity in tobacco Bright Yellow 2 cells indicates that reactive oxygen species (ROS) and nitric oxide, produced mainly via an l-arginine-dependent process, contribute to the kinase activation in response to cadmium. SnRK2.4 is the closest homolog of tobacco Osmotic Stress-Activated Protein Kinase in Arabidopsis (Arabidopsis thaliana). Comparative analysis of seedling growth of snrk2.4 knockout mutants versus wild-type Arabidopsis suggests that SnRK2.4 is involved in the inhibition of root growth triggered by cadmium; the mutants were more tolerant to the stress. Measurements of the level of three major species of phytochelatins (PCs) in roots of plants exposed to Cd2+ showed a similar (PC2, PC4) or lower (PC3) concentration in snrk2.4 mutants in comparison to wild-type plants. These results indicate that the enhanced tolerance of the mutants does not result from a difference in the PCs level. Additionally, we have analyzed ROS accumulation in roots subjected to Cd2+ treatment. Our data show significantly lower Cd2+-induced ROS accumulation in the mutants’ roots. Concluding, the obtained results indicate that SnRK2s play a role in the regulation of plant tolerance to cadmium, most probably by controlling ROS accumulation triggered by cadmium ions.
Composition and Physiological Function of the Wax Layers Coating Arabidopsis Leaves: β-Amyrin Negatively Affects the Intracuticular Water Barrier
Authors: Buschhaus Christopher , Jetter Reinhard
Published: August 2012

Plants prevent dehydration by coating their aerial, primary organs with waxes. Wax compositions frequently differ between species, organs, and developmental stages, probably to balance limiting nonstomatal water loss with various other ecophysiological roles of surface waxes. To establish structure-function relationships, we quantified the composition and transpiration barrier properties of the gl1 mutant leaf waxes of Arabidopsis (Arabidopsis thaliana) to the necessary spatial resolution. The waxes coating the upper and lower leaf surfaces had distinct compositions. Moreover, within the adaxial wax, the epicuticular layer contained more wax and a higher relative quantity of alkanes, whereas the intracuticular wax had a higher percentage of alcohols. The wax formed a barrier against nonstomatal water loss, where the outer layer contributed twice as much resistance as the inner layer. Based on this detailed description of Arabidopsis leaf waxes, structure-function relationships can now be established by manipulating one cuticle component and assessing the effect on cuticle functions. Next, we ectopically expressed the triterpenoid synthase gene AtLUP4 (for lupeol synthase4 or β-amyrin synthase) to compare water loss with and without added cuticular triterpenoids in Arabidopsis leaf waxes. β-Amyrin accumulated solely in the intracuticular wax, constituting up to 4% of this wax layer, without other concomitant changes of wax composition. This triterpenoid accumulation caused a significant reduction in the water barrier effectiveness of the intracuticular wax.
A Nitrogen-Regulated Glutamine Amidotransferase (GAT1_2.1) Represses Shoot Branching in Arabidopsis
Authors: Zhu Huifen , Kranz Robert G.
Published: August 2012

Shoot branching in plants is regulated by many environmental cues and by specific hormones such as strigolactone (SL). We show that the GAT1_2.1 gene (At1g15040) is repressed over 50-fold by nitrogen stress, and is also involved in branching control. At1g15040 is predicted to encode a class I glutamine amidotransferase (GAT1), a superfamily for which Arabidopsis (Arabidopsis thaliana) has 30 potential members. Most members can be categorized into known biosynthetic pathways, for the amidation of known acceptor molecules (e.g. CTP synthesis). Some members, like GAT1_2.1, are of unknown function, likely involved in amidation of unknown acceptors. A gat1_2.1 mutant exhibits a significant increase in shoot branching, similar to mutants in SL biosynthesis. The results suggest that GAT1_2.1 is not involved in SL biosynthesis since exogenously applied GR24 (a synthetic SL) does not correct the mutant phenotype. The subfamily of GATs (GATase1_2), with At1g15040 as the founding member, appears to be present in all plants (including mosses), but not other organisms. This suggests a plant-specific function such as branching control. We discuss the possibility that the GAT1_2.1 enzyme may activate SLs (e.g. GR24) by amidation, or more likely could embody a new pathway for repression of branching.
The Rice Wall-Associated Receptor-Like Kinase Gene OsDEES1 Plays a Role in Female Gametophyte Development
Authors: Wang Na , Huang Hui-Jia , Ren Su-Ting , Li Jiao-Jiao , Sun Ying , Sun Da-Ye , Zhang Su-Qiao
Published: August 2012

The wall-associated kinase (WAK) gene family is a unique subfamily of receptor-like kinases (RLKs) in plants. WAK-RLKs play roles in cell expansion, pathogen resistance, and metal tolerance in Arabidopsis (Arabidopsis thaliana). Rice (Oryza sativa) has far more WAK-RLK genes than Arabidopsis, but the functions of rice WAK-RLKs are poorly understood. In this study, we found that one rice WAK-RLK gene, DEFECT IN EARLY EMBRYO SAC1 (OsDEES1), is involved in the regulation of early embryo sac development. OsDEES1 silencing by RNA interference caused a high rate of female sterility. Crossing experiments showed that female reproductive organs lacking OsDEES1 carried a functional defect. A detailed investigation of the ovaries from OsDEES1 RNA interference plants indicated that the knockdown of OsDEES1 expression did not affect megasporogenesis but that it disturbed female gametophyte formation, resulting in a degenerated embryo sac and defective seed formation. OsDEES1 exhibited a tissue-specific expression pattern in flowers and seedlings. In the ovary, OsDEES1 was expressed in the megagametophyte region and surrounding nucellus cells in the ovule near the micropylar region. OsDEES1 was found to be a membrane-localized protein with a unique sequence compared with other WAK-RLKs. These data indicate that OsDEES1 plays a role in rice sexual reproduction by regulating female gametophyte development. This study offers new insight into the functions of the WAK-RLK family.
Reinterpretation of the monohydrate of clarithromycin from X-ray powder diffraction data as a trihydrate
Authors: Streek Jacco van de
Published: August 2012

Noguchi, Fujiki, Iwao, Miura & Itai [Acta Cryst.(2012), E68, o667–o668] recently reported the crystal structure of clarithromycin monohydrate from synchrotron X-ray powder diffraction data. Voids in the crystal structure suggested the possible presence of two more water molecules. After successful location of the two additional water molecules, the Rietveld refinement still showed minor problems. These were resolved by noticing that one of the chiral centres in the molecule had been inverted. The corrected crystal structure of clarithromycin trihydrate, refined against the original data, is now reported. Dispersion-corrected density functional theory calculations were used to check the final crystal structure and to position the H atoms.
Looking desperately for courage or how to study a polysemic concept
Authors: Harbour Michelle , Kisfalvi Veronika
Published: August 2012

Purpose

The purpose of this article is to propose an approach using mixed methods appropriate for studying polysemic concepts.

Design/methodology/approach

Anchored in cognitive approaches, the methods relied on a generally applicable conceptual framework, on cognitive mapping for an intellectualized conception, and on in‐depth interviews for an experiential conception on different participants’ judgments of managerial courage within the same context.

Findings

The mixed methods approach allowed the study first, to uncover two kinds of managerial courage. Second, while the intellectualized conceptions led to the enumeration of a greater number of positive consequences for third parties, the conceptions resulting from recollections of experiences focused more on the consequences for the protagonist. Third, the conceptual framework allowed the authors to distinguish between the results obtained from the two distinct data collection methods: the moral dimension, present in the more intellectualized cognitive maps, was largely absent from the consequences identified by participants in the conception of managerial courage resulting from experience.

Originality/value

This approach has provided two original methodological contributions. The first is the development of a widely applicable conceptual framework useful for studying polysemic concepts and for treating data generated by both approaches. The second is the distinction between conceptions of courage obtained from cognitive maps and those obtained through semi‐structured, in‐depth interviews, highlighting the complementarity of the chosen methods.
A multidimensional model for analyzing employee identification with corporate values
Authors: Agerholm Andersen Mona
Published: August 2012

Purpose

The purpose of this paper is to explore the use of a multidimensional model from the field of media reception for analyzing how a value statement in a Danish windmill company led to employee identification as well as organizational antecedents that influenced this identification. Further, the paper evaluates whether the proposed model can enhance understanding of the study of employee identification in a specific organizational situation and context.

Design/methodology/approach

The identification model extends a multidimensional model for media reception originally proposed by Schrøder in the field of media reception studies. The proposed model includes the following reception dimensions: comprehension, discrimination, implementation, motivation, and position.

Findings

This paper illustrates how employees from a Danish windmill company receive a value statement. A systematic application of the multidimensional model makes it possible to gain detailed insight into the active and complex process of employee identifications with organizational texts and how they may fluctuate in a specific context.

Research limitations/implications

This analysis only focuses on the reception of a value statement. Future research could include the analysis of employee readings of other types of organizational texts.

Originality/value

The multidimensional identification model is an extension of a media reception model and is new in the field of organizational identification. The model offers a method for analyzing the complexity and multiplicity of employee readings of different types of organizational texts. This may be crucial for both researchers and managers as the model may help to uncover the antecedents that influence how employees receive organizational texts while taking the historical and situational context of the organization into consideration.
Evidence for pathogenicity of autoreactive T cells in autoimmune bullous diseases shown by animal disease models
Authors: Ujiie Hideyuki , Shimizu Hiroshi
Published: August 2012

Autoimmune bullous diseases (AIBDs) are characterized by blisters and erosions on the skin and/or mucous membranes, which are caused by autoantibodies directed to structural proteins of the epidermis and the epidermal basement membrane zone. This Viewpoint Essay discusses the contribution by autoreactive T cells to the pathogenesis of bullous pemphigoid, pemphigus and epidermolysis bullosa acquisita, with an emphasis on studies using active animal mouse models for these diseases. Previous studies have demonstrated that cytokines produced by autoreactive T cells, the interaction between antigen‐specific T cells and B cells and the function of regulatory T cells are likely related to the pathogenesis of AIBDs. In interpreting the experimental results, the limitations of those animal models should be considered. Further understanding of the pathogenicity of autoreactive CD4+ T cells may lead to disease‐specific treatments.
B cell activating factor (BAFF) in the natural history of chronic hepatitis C virus liver disease and mixed cryoglobulinaemia
Authors: Lake-Bakaar G , Jacobson I , Talal A
Published: August 2012

B cell activating factor (BAFF) plays a crucial role in the process of development, maturation and activation of B lymphocytes. Chronic hepatitis C virus (HCV) infection is characterized by multiple B cell disorders. It is a major cause of type II mixed cryoglobulinaemia (MC). We measured serum BAFF levels in several clinical situations to elucidate the potential role of BAFF in chronic HCV infection. We used a commercially available solid phase enzyme-linked immunosorbent assay. We estimated serum BAFF in stored sera from uninfected controls (n = 8), patients with chronic hepatitis B virus infection HBV (n = 5) and chronic HCV infection with (n = 16) and without mixed cryoglobulinaemia (n = 14). In two patients with HCV and MC we correlated BAFF with HCV RNA after pegylated interferon (peg-I). We correlated serum BAFF levels at baseline and at 12 weeks with treatment response: sustained virological response SVR (n = 5), non-responders (n = 6) and relapsers (n = 2). Finally, we estimated BAFF levels after complete depletion of B cells with rituximab in patients with chronic HCV with MC (n = 3). Serum levels of BAFF were increased in chronic HCV with MC, but not in chronic HBV infection, suggesting an association between BAFF and cryoglobulinaemia. Peg-I increased BAFF levels in serum and this paralleled HCV RNA very closely. Serum BAFF levels at week 12 of therapy with peg-I and R were significantly higher in responders than non-responders. Finally, B cell depletion was associated with markedly increased levels of BAFF.
Thinning of large mammalian cells for cryo‐TEM characterization by cryo‐FIB milling
Authors: STRUNK K.M. , WANG K. , KE D. , GRAY J.L. , ZHANG P.
Published: August 2012

Focused ion beam milling at cryogenic temperatures (cryo‐FIB) is a valuable tool that can be used to thin vitreous biological specimens for subsequent imaging and analysis by cryo‐transmission electron microscopy (cryo‐TEM) in a frozen‐hydrated state. This technique offers the potential benefit of eliminating the mechanical artefacts that are typically found with cryo‐ultramicrotomy. However, due to the additional complexity in transferring samples in and out of the FIB, contamination and devitrification of the amorphous ice is commonly encountered. To address these problems, we have designed a sample cryo‐shuttle that directly and specifically accepts Polara TEM cartridges to simplify the transfer process between FIB and TEM. We optimized several parameters in the cryo‐FIB and cryo‐TEM processes using the quality of the samples’ ice as an indicator and demonstrated high‐quality milling with large mammalian cells. By comparing the results from HeLa cells to those from Escherichia coli cells, we discuss some of the artefacts and challenges we have encountered using this technique.
A line scanning confocal fluorescent microscope using a CMOS rolling shutter as an adjustable aperture
Authors: MEI E. , FOMITCHOV P.A. , GRAVES R. , CAMPION M.
Published: August 2012

Traditional confocal microscopy uses a physical aperture barrier to prevent out‐of‐focus light from reaching the detector. The physical nature of a conventional aperture limits control over the system confocality. We describe a new line scanning confocal microscope that eliminates a need for a physical aperture by employing a software‐controllable rolling shutter on a CMOS camera. A confocal image is obtained by synchronizing motion of the rolling shutter and the laser line scanning over a sample. Confocal resolution of this microscope is adjustable in real time and independently established for each fluorescence channel by changing the rolling shutter width. This technology has been implemented in the IN Cell Analyzer 6000 system by GE Healthcare.
Tooth and cranial disparity in the fossil relatives of Sphenodon (Rhynchocephalia) dispute the persistent ‘living fossil’ label
Authors: Meloro C. , Jones M. E. H.
Published: August 2012

The tuatara (Sphenodon punctatus) is the only living representative of Rhynchocephalia, a group of small vertebrates that originated about 250 million years ago. The tuatara has been referred to as a living fossil; however, the group to which it belongs included a much greater diversity of forms in the Mesozoic. We explore the morphological diversity of Rhynchocephalia and stem lepidosaur relatives (Sphenodon plus 13 fossil relatives) by employing a combination of geometric morphometrics and comparative methods. Geometric morphometrics is used to explore cranium size and shape at interspecific scale, while comparative methods are employed to test association between skull shape and size and tooth number after taking phylogeny into account. Two phylogenetic topologies have been considered to generate a phylomorphospace and quantify the phylogenetic signal in skull shape data, the ancestral state reconstruction as well as morphological disparity using disparity through time plots (DTT). Rhynchocephalia exhibit a significant phylogenetic signal in skull shape that compares well with that computed for other extinct vertebrate groups. A consistent form of allometry has little impact on skull shape evolution while the number of teeth significantly correlates with skull shape also after taking phylogeny into account. The ancestral state reconstruction demonstrates a dramatic shape difference between the skull of Sphenodon and its much larger Cretaceous relative Priosphenodon. Additionally, DTT demonstrates that skull shape disparity is higher between rather than within clades while the opposite applies to skull size and number of teeth. These results were not altered by the use of competing phylogenic hypotheses. Rhynchocephalia evolved as a morphologically diverse group with a dramatic radiation in the Late Triassic and Early Jurassic about 200 million years ago. Differences in size are not marked between species whereas changes in number of teeth are associated with co‐ordinated shape changes in the skull to accommodate larger masticatory muscles. These results show that the tuatara is not the product of evolutionary stasis but that it represents the only survivor of a diverse Mesozoic radiation whose subsequent decline remains to be explained.
Evidence for specificity to Glomus group Ab in two Asian mycoheterotrophic Burmannia species
Authors: Suetsugu Kenji , Kawakita Atsushi , Kato Makoto
Published: August 2012

Nonphotosynthetic mycorrhizal plants, so‐called mycoheterotrophic plants, have long attracted the curiosity of botanists and mycologists. Recent advances in molecular methods based on fungal‐specific PCR amplification have dramatically enhanced the identification of their host mycorrhizal fungi. However, studies investigating the fungal hosts of arbuscular mycorrhizae‐forming mycoheterotrophs are still limited in Asia, which is known as one of the diversity hot spots of mycoheterotrophs that parasitize arbuscular mycorrhizae (AM). Therefore, we aimed to reveal the mycorrhizal associations of two Asian, fully mycoheterotrophic Burmannia species by molecular identification. Sequences of the small subunit ribosomal DNA showed that both Burmannia species are associated with several distinct lineages of Glomus group Ab. Because Glomus group Ab fungi have been confirmed as fungal hosts of various mycoheterotrophic plants in Africa and South America, we suggest they are widely exploited by AM‐forming mycoheterotrophs globally.
Diagnosis of autism spectrum disorders in 2‐year‐olds: a study of community practice
Authors: Corsello Christina M. , Akshoomoff Natacha , Stahmer Aubyn C.
Published: August 2012

Background:  Longitudinal research studies have demonstrated that experienced clinicians using standardized assessment measures can make a reliable diagnosis of autism spectrum disorders (ASDs) in children under age 3. Limited data are available regarding the sensitivity and specificity of these measures in community settings. The aims of this study were to determine how well a standardized diagnostic observational measure (Autism Diagnostic Observation Schedule – ADOS) functions alone, and with a brief parent measure within a community setting when administered by community clinicians.

Methods:  Clinical records for 138 children between the ages of 24 and 36 months of age who were evaluated for possible ASD or social/language concerns at a hospital‐based developmental evaluation clinic were examined. Evaluations were conducted by community‐based clinical psychologists. Classification results obtained from standardized diagnostic measures were compared with case reviewer diagnosis, by reviewers blind to scores on diagnostic measures, using The Records‐based Methodology for ASD Case Definition that was developed by the Metropolitan Atlanta Developmental Disabilities Surveillance Program.

Results:  When compared with case review diagnosis, the ADOS demonstrated strong sensitivity and specificity for both Autism versus Not Autism and ASD versus Nonspectrum (NS) diagnoses in this young sample. The Social Communication Questionnaire (SCQ), using the lower cutoff of ≥12, had adequate sensitivity when differentiating Autism from Not Autism, but weak sensitivity when differentiating ASD from NS, missing about 80% of the children with pervasive developmental disorder – not otherwise specified. Using either the Modified Checklist for Autism in Toddlers or the SCQ in combination with the ADOS did not result in improved specificity over the ADOS alone and led to a drop in sensitivity when differentiating ASD from NS disorders.

Conclusions:  These results demonstrate that following best practice guidelines, the ADOS can be successfully incorporated into clinical practice with relatively good sensitivity and specificity, and worked well with a referred sample of 2‐year‐olds. A parent questionnaire did not lead to any improvement in diagnostic classification above the ADOS used in isolation.