bluuebunny/crossref_metadata_2025_split huggingface dataset:
The DROOPING LEAF and OsETTIN2 genes promote awn development in rice
Authors: Toriba Taiyo , Hirano Hiro‐Yuki 
Published: December 2013

SummaryThe awn is a long needle‐like appendage that, in some grass species, is formed on the lemma that encloses floral organs together with the palea. In rice, most wild species and most strains of Oryza sativa ssp. indica generate an awn, whereas most strains of O. sativa ssp. japonica do not. In japonica, the long‐awn characteristic appears to have been lost during domestication and breeding programs. Here, we found that the genes DROOPING LEAF (DL) and OsETTIN2 (OsETT2) are involved in awn development in the awned indica strain Kasalath. Genetic analyses and RNA‐silencing experiments indicate that DL and OsETT2 act independently in awn formation, and that either gene alone is not sufficient for awn development. Scanning electron microscopy revealed that the top region of the lemma (a putative awn primordium) is larger in an awned floret than in an awnless floret. OsETT2 is expressed in the awn primordium in the awned indica floret, but not in the awnless japonica floret except in the provascular bundle. DL is expressed underneath the primordium at similar levels in both indica and japonica florets, suggesting non‐cell‐autonomous action. We hypothesize that loss of expression of OsETT2 in the awn primordium is probably associated with the failure of awn formation in japonica strains.
Comparative BAC‐based physical mapping of Oryza sativa ssp. indica var. 93–11 and evaluation of the two rice reference sequence assemblies
Authors: Pan Yonglong , Deng Ying , Lin Haiyan , Kudrna David A. , Wing Rod A. , Li Lijia , Zhang Qifa , Luo Meizhong 
Published: December 2013

SummaryReference sequences are sequences that are used for public consultation, and therefore must be of high quality. Using the whole‐genome shotgun/next‐generation sequencing approach, many genome sequences of complex higher plants have been generated in recent years, and are generally considered reference sequences. However, none of these sequences has been experimentally evaluated at the whole‐genome sequence assembly level. Rice has a relatively simple plant genome, and the genome sequences for its two sub‐species obtained using different sequencing approaches were published approximately 10 years ago. This provides a unique system for a case study to evaluate the qualities and utilities of published plant genome sequences. We constructed a robust BAC physical map embedding a large number of BAC end sequences forrice variety 93–11. Through BAC end sequence alignments and tri‐assembly comparisons of the 93–11 physical map and the two reference sequences, we found that the Nipponbare reference sequence generated using the clone‐by‐clone approach has a high quality but still contains small artifact inversions and missing sequences. In contrast, the 93–11 reference sequence generated using the whole‐genome shotgun approach contains many large and varied assembly errors, such as inversions, duplications and translocations, as well as missing sequences. The 93–11 physical map provides an invaluable resource for evaluation and improvements toward completion of both Nipponbare and 93–11 reference sequences.
Precise plant breeding using new genome editing techniques: opportunities, safety and regulation in the EU
Authors: Hartung Frank , Schiemann Joachim 
Published: December 2013

SummarySeveral new plant breeding techniques (NPBTs) have been developed during the last decade, and make it possible to precisely perform genome modifications in plants. The major problem, other than technical aspects, is the vagueness of regulation concerning these new techniques. Since the definition of eight NPBTs by a European expert group in 2007, there has been an ongoing debate on whether the resulting plants and their products are covered by GMO legislation. Obviously, cover by GMO legislation would severely hamper the use of NPBT, because genetically modified plants must pass a costly and time‐consuming GMO approval procedure in the EU. In this review, we compare some of the NPBTs defined by the EU expert group with classical breeding techniques and conventional transgenic plants. The list of NPBTs may be shortened (or extended) during the international discussion process initiated by the Organization for Economic Co‐operation and Development. From the scientific point of view, it may be argued that plants developed by NPBTs are often indistinguishable from classically bred plants and are not expected to possess higher risks for health and the environment. In light of the debate on the future regulation of NPBTs and the accumulated evidence on the biosafety of genetically modified plants that have been commercialized and risk‐assessed worldwide, it may be suggested that plants modified by crop genetic improvement technologies, including genetic modification, NPBTs or other future techniques, should be evaluated according to the new trait and the resulting end product rather than the technique used to create the new plant variety.
Prevalence of restless legs syndrome in female blood donors 1 week after blood donation
Authors: Pedrazzini B. , Waldvogel S. , Vaucher P. , Cornuz J. , Heinzer R. , Tissot J.‐D. , Favrat B. 
Published: December 2013

Background and ObjectiveRestless legs syndrome (RLS) is a frequent condition with a prevalence of 5–15% in the general population. Clinical and genetic observations have shown that iron deficiency, highly prevalent among blood donors, can be related to RLS. The objective of this study was to assess the prevalence of RLS in female blood donors 1 week after blood donation.MethodsOne week after blood donation, 291 female blood donors, aged <50 years, self‐responded to all four RLS questions defined by the 1995 International RLS study group. Blood donation rate, fatigue, aerobic capacity, menstruation, mood disorder and quality of life were also assessed along with haemoglobin and ferritin blood concentrations.ResultsPrevalence of RLS in female blood donors 1 week after blood donation was 6·9% (CI 95% 4·2–10·4%). Female blood donors with RLS had a higher prevalence of hyper‐menorrhaea (P = 0·033) and were significantly more tired (P = 0·001). We observed no associations between RLS and number of previous donations (P = 0·409), aerobic capacity (P = 0·476), mood disorder (P = 0·169), quality of life (P = 0·356), haemoglobin (P = 0·087), and serum ferritin level (P = 0·446).ConclusionRestless legs syndrome prevalence in female blood donors is not as important as described in some other studies, which could reassure blood donors. The prevalence of hypermenorrhaea and fatigue is higher in RLS blood donors. Therefore, screening for fatigue and hypermenorrhaea could be considered as these symptoms are associated with RLS in female blood donors.
Amalgamated free product type III factors with at most one Cartan subalgebra
Authors: Boutonnet Rémi , Houdayer Cyril , Raum Sven 
Published: December 2013

AbstractWe investigate Cartan subalgebras in nontracial amalgamated free product von Neumann algebras ${\mathop{M{}_{1} \ast }\nolimits}_{B} {M}_{2} $ over an amenable von Neumann subalgebra $B$. First, we settle the problem of the absence of Cartan subalgebra in arbitrary free product von Neumann algebras. Namely, we show that any nonamenable free product von Neumann algebra $({M}_{1} , {\varphi }_{1} )\ast ({M}_{2} , {\varphi }_{2} )$ with respect to faithful normal states has no Cartan subalgebra. This generalizes the tracial case that was established by A. Ioana [Cartan subalgebras of amalgamated free product ${\mathrm{II} }_{1} $factors, arXiv:1207.0054]. Next, we prove that any countable nonsingular ergodic equivalence relation $ \mathcal{R} $ defined on a standard measure space and which splits as the free product $ \mathcal{R} = { \mathcal{R} }_{1} \ast { \mathcal{R} }_{2} $ of recurrent subequivalence relations gives rise to a nonamenable factor $\mathrm{L} ( \mathcal{R} )$ with a unique Cartan subalgebra, up to unitary conjugacy. Finally, we prove unique Cartan decomposition for a class of group measure space factors ${\mathrm{L} }^{\infty } (X)\rtimes \Gamma $ arising from nonsingular free ergodic actions $\Gamma \curvearrowright (X, \mu )$ on standard measure spaces of amalgamated groups $\Gamma = {\mathop{\Gamma {}_{1} \ast }\nolimits}_{\Sigma } {\Gamma }_{2} $ over a finite subgroup $\Sigma $.
Phylogeography of Cylindrospermopsin and Paralytic Shellfish Toxin-Producing Nostocales Cyanobacteria from Mediterranean Europe (Spain)
Authors: Cirés Samuel , Wörmer Lars , Ballot Andreas , Agha Ramsy , Wiedner Claudia , Velázquez David , Casero María Cristina , Quesada Antonio 
Published: December 2013

ABSTRACT

Planktonic
Nostocales
cyanobacteria represent a challenge for microbiological research because of the wide range of cyanotoxins that they synthesize and their invasive behavior, which is presumably enhanced by global warming. To gain insight into the phylogeography of potentially toxic
Nostocales
from Mediterranean Europe, 31 strains of
Anabaena
(
Anabaena crassa
,
A. lemmermannii
,
A. mendotae
, and
A. planctonica
),
Aphanizomenon
(
Aphanizomenon gracile
,
A. ovalisporum
), and
Cylindrospermopsis raciborskii
were isolated from 14 freshwater bodies in Spain and polyphasically analyzed for their phylogeography, cyanotoxin production, and the presence of cyanotoxin biosynthesis genes. The potent cytotoxin cylindrospermopsin (CYN) was produced by all 6
Aphanizomenon ovalisporum
strains at high levels (5.7 to 9.1 μg CYN mg
−1
[dry weight]) with low variation between strains (1.5 to 3.9-fold) and a marked extracellular release (19 to 41% dissolved CYN) during exponential growth. Paralytic shellfish poisoning (PSP) neurotoxins (saxitoxin, neosaxitoxin, and decarbamoylsaxitoxin) were detected in 2
Aphanizomenon gracile
strains, both containing the
sxtA
gene. This gene was also amplified in non-PSP toxin-producing
Aphanizomenon gracile
and
Aphanizomenon ovalisporum
. Phylogenetic analyses supported the species identification and confirmed the high similarity of Spanish
Anabaena
and
Aphanizomenon
strains with other European strains. In contrast,
Cylindrospermopsis raciborskii
from Spain grouped together with American strains and was clearly separate from the rest of the European strains, raising questions about the current assumptions of the phylogeography and spreading routes of
C. raciborskii
. The present study confirms that the nostocalean genus
Aphanizomenon
is a major source of CYN and PSP toxins in Europe and demonstrates the presence of the
sxtA
gene in CYN-producing
Aphanizomenon ovalisporum
.
The Legionella pneumophila Collagen-Like Protein Mediates Sedimentation, Autoaggregation, and Pathogen-Phagocyte Interactions
Authors: Abdel-Nour Mena , Duncan Carla , Prashar Akriti , Rao Chitong , Ginevra Christophe , Jarraud Sophie , Low Donald E. , Ensminger Alexander W. , Terebiznik Mauricio R. , Guyard Cyril 
Published: December 2013

ABSTRACT

Although only partially understood, multicellular behavior is relatively common in bacterial pathogens. Bacterial aggregates can resist various host defenses and colonize their environment more efficiently than planktonic cells. For the waterborne pathogen
Legionella pneumophila
, little is known about the roles of autoaggregation or the parameters which allow cell-cell interactions to occur. Here, we determined the endogenous and exogenous factors sufficient to allow autoaggregation to take place in
L. pneumophila
. We show that isolates from
Legionella
species which do not produce the
Legionella
collagen-like protein (Lcl) are deficient in autoaggregation. Targeted deletion of the Lcl-encoding gene (
lpg2644
) and the addition of Lcl ligands impair the autoaggregation of
L. pneumophila
. In addition, Lcl-induced autoaggregation requires divalent cations.
Escherichia coli
producing surface-exposed Lcl is able to autoaggregate and shows increased biofilm production. We also demonstrate that
L. pneumophila
infection of
Acanthamoeba castellanii
and
Hartmanella vermiformis
is potentiated under conditions which promote Lcl dependent autoaggregation. Overall, this study shows that
L. pneumophila
is capable of autoaggregating in a process that is mediated by Lcl in a divalent-cation-dependent manner. It also reveals that Lcl potentiates the ability of
L. pneumophila
to come in contact, attach, and infect amoebae.
The Third Replicon of Members of the Burkholderia cepacia Complex, Plasmid pC3, Plays a Role in Stress Tolerance
Authors: Agnoli Kirsty , Frauenknecht Carmen , Freitag Roman , Schwager Stephan , Jenul Christian , Vergunst Annette , Carlier Aurelien , Eberl Leo 
Published: December 2013

ABSTRACTThe metabolically versatileBurkholderia cepaciacomplex (Bcc) occupies a variety of niches, including the plant rhizosphere and the cystic fibrosis lung (where it is often fatal to the patient). Bcc members have multipartite genomes, of which the third replicon, pC3 (previously chromosome 3), has been shown to be a nonessential megaplasmid which confers virulence and both antifungal and proteolytic activity on several strains. In this study, pC3 curing was extended to cover strains of 16 of the 17 members of the Bcc, and the phenotypes conferred by pC3 were determined.B. cenocepaciastrains H111, MCO-3, and HI2424 were previously cured of pC3; however, this had not proved possible in the epidemic strain K56-2. Here, we investigated the mechanism of this unexpected stability and found that efficient toxin-antitoxin systems are responsible for maintaining pC3 of strain K56-2. Identification of these systems allowed neutralization of the toxins and the subsequent deletion of K56-2pC3. The cured strain was found to exhibit reduced antifungal activity and was attenuated in both the zebrafish and theCaenorhabditis elegansmodel of infection. We used a PCR screening method to examine the prevalence of pC3 within 110 Bcc isolates and found that this replicon was absent in only four cases, suggesting evolutionary fixation. It is shown that plasmid pC3 increases the resistance ofB. cenocepaciaH111 to various stresses (oxidative, osmotic, high-temperature, and chlorhexidine-induced stresses), explaining the prevalence of this replicon within the Bcc.
Role of the Apt1 Protein in Polysaccharide Secretion by Cryptococcus neoformans
Authors: Rizzo Juliana , Oliveira Débora L. , Joffe Luna S. , Hu Guanggan , Gazos-Lopes Felipe , Fonseca Fernanda L. , Almeida Igor C. , Frases Susana , Kronstad James W. , Rodrigues Marcio L. 
Published: December 2013

ABSTRACT

Flippases are key regulators of membrane asymmetry and secretory mechanisms. Vesicular polysaccharide secretion is essential for the pathogenic mechanisms of
Cryptococcus neoformans
. On the basis of the observations that flippases are required for polysaccharide secretion in plants and the putative Apt1 flippase is required for cryptococcal virulence, we analyzed the role of this enzyme in polysaccharide release by
C. neoformans
, using a previously characterized
apt1
Δ mutant. Mutant and wild-type (WT) cells shared important phenotypic characteristics, including capsule morphology and dimensions, glucuronoxylomannan (GXM) composition, molecular size, and serological properties. The
apt1
Δ mutant, however, produced extracellular vesicles (EVs) with a lower GXM content and different size distribution in comparison with those of WT cells. Our data also suggested a defective intracellular GXM synthesis in mutant cells, in addition to changes in the architecture of the Golgi apparatus. These findings were correlated with diminished GXM production during
in vitro
growth, macrophage infection, and lung colonization. This phenotype was associated with decreased survival of the mutant in the lungs of infected mice, reduced induction of interleukin-6 (IL-6) cytokine levels, and inefficacy in colonization of the brain. Taken together, our results indicate that the lack of
APT1
caused defects in both GXM synthesis and vesicular export to the extracellular milieu by
C. neoformans
via processes that are apparently related to the pathogenic mechanisms used by this fungus during animal infection.
Detailed Identification of Fatty Acid Isomers Sheds Light on the Probable Precursors of Triacylglycerol Accumulation in Photoautotrophically Grown Chlamydomonas reinhardtii
Authors: Sakurai Kenta , Moriyama Takashi , Sato Naoki 
Published: December 2013

ABSTRACT

Chlamydomonas reinhardtii
is a model alga for studying triacylglycerol (TAG) accumulation in the photosynthetic production of biofuel. Previous studies were conducted under photoheterotrophic growth conditions in medium supplemented with acetate and/or ammonium. We wanted to demonstrate TAG accumulation under truly photoautotrophic conditions without reduced elements. We first reidentified all lipid components and fatty acids by mass spectrometry, because the currently used identification knowledge relies on data obtained in the 1980s. Accordingly, various isomers of fatty acids, which are potentially useful in tracing the flow of fatty acids leading to the accumulation of TAG, were detected. In strain CC1010 grown under photoautotrophic conditions, TAG accumulated to about 57.5 mol% of total lipids on a mole fatty acid basis after the transfer to nitrogen-deficient conditions. The content of monogalactosyl diacylglycerol, sulfoquinovosyl diacylglycerol, and phosphatidylglycerol decreased drastically. The accumulated TAG contained 16:0 as the major acid and 16:4(4,7,10,13), 18:2(9,12), and 18:3(9,12,15), which are typically found in chloroplast lipids. Additionally, 18:1(11) and 18:3(5,9,12), which are specific to extrachloroplast lipids, were also abundant in the accumulated TAG. Photosynthesis and respiration slowed markedly after the shift to nitrogen-deficient conditions. These results suggest that fatty acids for the production of TAG were supplied not only from chloroplast lipids but also from other membranes within the cells, although the possibility of
de novo
synthesis cannot be excluded. Under nitrogen-replete conditions, supplementation with a high concentration of CO
2
promoted TAG production in the cells grown photoautotrophically, opening up the possibility to the continuous production of TAG using CO
2
produced by industry.
Draft Genome Sequence of
Enterococcus
sp. Strain HSIEG1, Isolated from the Human Small Intestine
Authors: van den Bogert Bartholomeus , Boekhorst Jos , Smid Eddy J. , Zoetendal Erwin G. , Kleerebezem Michiel 
Published: December 2013

ABSTRACT

Enterococcus
sp. strain HSIEG1 was isolated from the human small intestine. Its draft genome predicts a broad carbohydrate fermentation capability, which matches well with the observed physiological characteristics of this strain. This metabolic flexibility is expected to be of importance for survival and growth in the small intestinal habitat.
The EutT Enzyme of Salmonella enterica Is a Unique ATP:Cob(I)alamin Adenosyltransferase Metalloprotein That Requires Ferrous Ions for Maximal Activity
Authors: Moore Theodore C. , Mera Paola E. , Escalante-Semerena Jorge C. 
Published: December 2013

ABSTRACT

ATP:co(I)rrinoid adenosyltransferase (ACAT) enzymes convert vitamin B
12
to coenzyme B
12
. EutT is the least understood ACAT. We report the purification of EutT to homogeneity and show that,
in vitro
, free dihydroflavins drive the adenosylation of cob(II)alamin bound to EutT. Results of chromatography analyses indicate that EutT is dimeric in solution, and unlike other ACATs, EutT catalyzes the reaction with sigmoidal kinetics indicative of positive cooperativity for cob(II)alamin. Maximal EutT activity was obtained after metalation with ferrous ions. EutT/Fe(II) protein lost all activity upon exposure to air and H
2
O
2
, consistent with previously reported results indicating that EutT was an oxygen-labile metalloprotein containing a redox-active metal. Results of
in vivo
and
in vitro
analyses of single-amino-acid variants affecting a HX
11
CCXXC
83
motif conserved in EutT proteins showed that residues His67, Cys80, and Cys83 were required for EutT function
in vivo
, while Cys79 was not. Unlike that of other variants, the activity of the EutT
C80A
variant was undetectable
in vitro
, suggesting that Cys80 was critical to EutT function. Results of circular dichroism studies indicate that the presence or absence of a metal ion does not affect protein folding. EutT can now be purified in the presence of oxygen and reactivated with ferrous ions for maximal activity.
Profile, cost and pattern of prescriptions for polymedicated patients in Catalonia, Spain
Authors: Lizano-Díez Irene , Modamio Pilar , López-Calahorra Pilar , Lastra Cecilia F , Gilabert-Perramon Antoni , Segú Jose L , Mariño Eduardo L 
Published: December 2013

ObjectivesPolypharmacy is one of the main management issues in public health policies because of its financial impact and the increasing number of people involved. The polymedicated population according to their demographic and therapeutic profile and the cost for the public healthcare system were characterised.DesignCross-sectional study.SettingPrimary healthcare in Barcelona Health Region, Catalonia, Spain (5 105 551 inhabitants registered).ParticipantsAll insured polymedicated patients. Polymedicated patients were those with a consumption of ≥16 drugs/month.Main outcomes measuresThe study variables were related to age, gender and medication intake obtained from the 2008 census and records of prescriptions dispensed in pharmacies and charged to the public health system.ResultsThere were 36 880 polymedicated patients (women: 64.2%; average age: 74.5±10.9 years). The total number of prescriptions billed in 2008 was 2 266 830 (2 272 920 total package units). The most polymedicated group (up to 40% of the total prescriptions) was patients between 75 and 84 years old. The average number of prescriptions billed monthly per patient was 32±2, with an average cost of €452.7±27.5. The total cost of those prescriptions corresponded to 2% of the drug expenditure in Catalonia. The groups N, C, A, R and M represented 71.4% of the total number of drug package units dispensed to polymedicated patients. Great variability was found between the medication profiles of men and women, and between age groups; greater discrepancies were found in paediatric patients (5–14 years) and the elderly (≥65 years).ConclusionsThis study provides essential information to take steps towards rational drug use and a structured approach in the polymedicated population in primary healthcare.