bluuebunny/crossref_metadata_2025_split huggingface dataset:
ROP11 GTPase is a Negative Regulator of Multiple ABA Responses in Arabidopsis
Authors: Li Zixing , Kang Jun , Sui Ning , Liu Dong 
Published: January 2012

AbstractThe phytohormone abscisic acid (ABA) plays crucial roles in plant development and plant responses to environmental stresses. Although ABA receptors and a minimal set of core molecular components have recently been discovered, understanding of the ABA signaling pathway is still far from complete. In this work, we characterized the function of ROP11, a member of the plant‐specific ROP small GTPases family, in the ABA signaling process. ROP11 is preferentially expressed in guard cells in all plant organs with stomata. Expression of a constitutively active ROP11 (CA‐ROP11) suppresses ABA‐mediated responses, whereas reduced expression of ROP11 or expression of its dominant‐negative form (DN‐ROP11) causes the opposite phenotypes. The affected ABA‐mediated responses by ROP11 include seed germination, seedling growth, stomatal closure, induction of ABA‐responsive genes, as well as plant response to drought stress. Furthermore, we showed that ROP11 and its closest‐related family member, ROP10, act in parallel in mediating these responses. ABA treatment does not affect ROP11 transcription and protein abundance; however, it causes the accumulation of CA‐ROP11 in the nucleus. These results demonstrated that ROP11 is a negative regulator of multiple ABA responses in Arabidopsis.
Statistics Research at Bell Labs in the Regulated Monopoly Era
Authors: Kettenring Jon R. 
Published: January 2012

RésuméL'essor et le développement de la recherche industrielle aux Etats‐Unis couvrent une grande partie du 20e siècle. Les Bell Labs, composante du Bell System, en sont peut‐être le meilleur exemple. La période qui s'étend de leur création en 1925 à leur démantèlement en 1984—suite à des poursuites judiciaires relatives aux lois anti‐trust—est d'un intérêt tout particulier. Le système, pendant cette époque, a en effet été géréà la manière d'un monopole, les abonnés soutenant réellement, au travers de leurs factures téléphoniques mensuelles, les activités de recherche et développement, procurant ainsi aux Bell Labs une grande stabilité financière. La statistique figure parmi les domaines de recherche les plus florissants des Labs, pour le plus grand bénéfice du Bell System, de ses clients, et de la science statistique. Le but de cet article est de passer en revue, d'expliquer et d'illustrer les circonstances de ce succès, tout en s'interrogeant sur la façon dont les entreprises modernes, dans le contexte concurrentiel qui est le leur, pourraient s'assurer le même type d'avantages.
Endobronchial valve deployment in severe α‐1 antitrypsin deficiency emphysema: a case series
Authors: Tuohy Mary Majella , Remund Kasper Friedrich , Hilfiker Roger , Murphy Dara Thomas , Murray John Gerard , Egan Jim John 
Published: January 2012

AbstractIntroduction:  Patients with end‐stage emphysema because of α‐1 antitrypsin (AAT) deficiency represent a challenging clinical management problem, and studies of volume reduction therapy to date have largely excluded these patients. We report the outcome of bronchoscopic volume reduction with the insertion of Emphasys endobronchial valves (Emphasys Medical, Redwood City, CA, USA) in six patients with end‐stage emphysema because of AAT deficiency.Case Series:  Of 51 patients with end stage emphysema referred for transplantation, we studied six patients with AAT deficiency and utilized the BODE index and lung allocation score for survival estimation.Measurements and Main Results:  The forced expiratory volume in 1 s improved from a median of 0.575 L to 0.905 L (P = 0.028). There was a median reduction in total lung capacity (TLC) of 0.61 L. The residual volume /TLC fell from 74.0% to 58.4%. Before treatment, four patients had a BODE index of greater than eight units, which correlates with a 4‐year survival of 18%. After treatment, two patients improved their BODE index to below seven units, which correlates with an estimated 4‐year survival of over 50%.Conclusions:  The data from this case series suggest that this intervention may provide bridging therapy to subsequent transplantation for younger AAT patients with end‐stage emphysema.Please cite this paper as: Tuohy MM, Remund KF, Hilfiker R, Murphy DT, Murray JG and Egan JJ. Endobronchial valve deployment in severe α‐1 antitrypsin deficiency emphysema: a case series. Clin Respir J 2013; 7: 45–52.
Integrative taxonomy at work: DNA barcoding of taeniids harboured by wild and domestic cats
Authors: GALIMBERTI A. , ROMANO D. F. , GENCHI M. , PAOLONI D. , VERCILLO F. , BIZZARRI L. , SASSERA D. , BANDI C. , GENCHI C. , RAGNI B. , CASIRAGHI M. 
Published: January 2012

AbstractIn modern taxonomy, DNA barcoding is particularly useful where biometric parameters are difficult to determine or useless owing to the poor quality of samples. These situations are frequent in parasitology. Here, we present an integrated study, based on both DNA barcoding and morphological analysis, on cestodes belonging to the genus Taenia, for which biodiversity is still largely underestimated. In particular, we characterized cestodes from Italian wildcats (Felis silvestris silvestris), free‐ranging domestic cats (Felis silvestris catus) and hybrids populations. Adult taeniids were collected by post‐mortem examinations of the hosts and morphologically identified as Taenia taeniaeformis. We produced cox1 barcode sequences for all the analysed specimens, and we compared them with reference sequences of individuals belonging to the genus Taenia retrieved from GenBank. In order to evaluate the performance of a DNA barcoding approach to discriminate these parasites, the strength of correlation between species identification based on classical morphology and the molecular divergence of cox1 sequences was measured. Our study provides clear evidence that DNA barcoding is highly efficient to reveal the presence of cryptic lineages within already‐described taeniid species. Indeed, we detected three well‐defined molecular lineages within the whole panel of specimens morphologically identified as T. taeniaeformis. Two of these molecular groups were already identified by other authors and should be ranked at species level. The third molecular group encompasses only samples collected in Italy during this study, and it represents a third candidate species, still morphologically undescribed.
Targeting sphingosine kinase‐1 to inhibit melanoma
Authors: Madhunapantula SubbaRao V. , Hengst Jeremy , Gowda Raghavendra , Fox Todd E. , Yun Jong K. , Robertson Gavin P. 
Published: January 2012

SummaryResistance to therapies develops rapidly for melanoma leading to more aggressive disease. Therefore, agents are needed that specifically inhibit proteins or pathways controlling the development of this disease, which can be combined, dependent on genes deregulated in a particular patient’s tumors. This study shows that elevated sphingosine‐1‐phosphate (S‐1‐P) levels resulting from increased activity of sphingosine kinase‐1 (SPHK1) occur in advanced melanomas. Targeting SPHK1 using siRNA decreased anchorage‐dependent and ‐independent growth as well as sensitized melanoma cells to apoptosis‐inducing agents. Pharmacological SPHK1 inhibitors SKI‐I but not SKI‐II decreased S‐1‐P content, elevated ceramide levels, caused a G2‐M block and induced apoptotic cell death in melanomas. Targeting SPHK1 using siRNA or the pharmacological agent called SKI‐I decreased the levels of pAKT. Furthermore, SKI‐I inhibited the expression of CYCLIN D1 protein and increased the activity of caspase‐3/7, which in turn led to the degradation of PARP. In animals, SKI‐I but not SKI‐II retarded melanoma growth by 25–40%. Thus, targeting SPHK1 using siRNAs or SKI‐I has therapeutic potential for melanoma treatment either alone or in combination with other targeted agents.
Personality differences in mental imagery and the effects on verbal memory
Authors: McDougall Siné , Pfeifer Gaby 
Published: January 2012

This study examined the effects of extraversion and neuroticism on participants’ reported vividness of visual imagery and on their memory performance for concrete and abstract nouns. Groups of extraverts (n = 15) and introverts (n = 15) were selected from a larger original sample and asked to remember a series of concrete and abstract nouns, including a set of lexically ambiguous concrete homonyms (e.g., earth = 1. planet, 2. soil). Extraverts reported more vivid imagery than introverts but this did not translate into better recall for extraverts, even for concrete stimuli. Recall was best for unambiguous concrete nouns, followed by concrete homonyms, then abstract nouns. While initial analyses suggested that there was an interaction between extraversion and the type of word presented, later analyses revealed that neuroticism was the main driver in differences in recall between different word types. While differences in recall were best explained by context availability theory (Schwanenflugel, 1991) rather than dual coding theory (Paivio, 1991), questions remain about the power of either theory to explain the role of individual differences in personality on recall, particularly given that imagery vividness effects were related to extraversion while differences in recall were related to neuroticism. The implications of these findings for future research and theoretical development are discussed.
Rhodococcus sp. Strain CR-53 LipR, the First Member of a New Bacterial Lipase Family (Family X) Displaying an Unusual Y-Type Oxyanion Hole, Similar to the Candida antarctica Lipase Clan
Authors: Bassegoda Arnau , Pastor F. I. Javier , Diaz Pilar 
Published: January 2012

ABSTRACT

Bacterial lipases constitute the most important group of biocatalysts for synthetic organic chemistry. Accordingly, there is substantial interest in developing new valuable lipases. Considering the lack of information concerning the lipases of the genus
Rhodococcus
and taking into account the interest raised by the enzymes produced by actinomycetes, a search for putative lipase-encoding genes from
Rhodococcus
sp. strain CR-53 was performed. We isolated, cloned, purified, and characterized LipR, the first lipase described from the genus
Rhodococcus
. LipR is a mesophilic enzyme showing preference for medium-chain-length acyl groups without showing interfacial activation. It displays good long-term stability and high tolerance for the presence of ions and chemical agents in the reaction mixture. Amino acid sequence analysis of LipR revealed that it displays four unique amino acid sequence motifs that clearly separate it from any other previously described family of bacterial lipases. Using bioinformatics tools, LipR could be related only to several uncharacterized putative lipases from different bacterial origins, all of which display the four blocks of consensus amino acid sequence motifs that contribute to define a new family of bacterial lipases, namely, family X. Therefore, LipR is the first characterized member of the new bacterial lipase family X. Further confirmation of this new family of lipases was performed after cloning
Burkholderia cenocepacia
putative lipase, bearing the same conserved motifs and clustering in family X. Interestingly, all lipases grouping in the new bacterial lipase family X display a Y-type oxyanion hole, a motif conserved in the
Candida antarctica
lipase clan but never found among bacterial lipases. This observation contributes to confirm that LipR and its homologs belong to a new family of bacterial lipases.
Characterization of Two Bacterial Hydroxynitrile Lyases with High Similarity to Cupin Superfamily Proteins
Authors: Hussain Zahid , Wiedner Romana , Steiner Kerstin , Hajek Tanja , Avi Manuela , Hecher Bianca , Sessitsch Angela , Schwab Helmut 
Published: January 2012

ABSTRACT

Hydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrins. In the reverse reaction, they catalyze the formation of carbon-carbon bonds by enantioselective condensation of hydrocyanic acid with carbonyls. In this study, we describe two proteins from endophytic bacteria that display activity in the cleavage and the synthesis reaction of (
R
)-mandelonitrile with up to 74% conversion of benzaldehyde (enantiopreference
ee
89%). Both showed high similarity to proteins of the cupin superfamily which so far were not known to exhibit HNL activity.
Abundance, Dynamics, and Biogeographic Distribution of Seven Polycyclic Aromatic Hydrocarbon Dioxygenase Gene Variants in Coastal Sediments of Patagonia
Authors: Marcos Magalí S. , Lozada Mariana , Di Marzio Walter D. , Dionisi Hebe M. 
Published: January 2012

ABSTRACT

Novel polycyclic aromatic hydrocarbon dioxygenase gene variants were present in abundances similar to or higher than those of
phnA1
from
Cycloclasticus
spp. at a chronically polluted subantarctic coastal marine environment in Patagonia. These novel gene variants were detected over a 6-year time span and were also present in sediments from temperate Patagonian sites.
Aerosol Susceptibility of Influenza Virus to UV-C Light
Authors: McDevitt James J. , Rudnick Stephen N. , Radonovich Lewis J. 
Published: January 2012

ABSTRACT

The person-to-person transmission of influenza virus, especially in the event of a pandemic caused by a highly virulent strain of influenza, such as H5N1 avian influenza, is of great concern due to widespread mortality and morbidity. The consequences of seasonal influenza are also substantial. Because airborne transmission appears to play a role in the spread of influenza, public health interventions should focus on preventing or interrupting this process. Air disinfection via upper-room 254-nm germicidal UV (UV-C) light in public buildings may be able to reduce influenza transmission via the airborne route. We characterized the susceptibility of influenza A virus (H1N1, PR-8) aerosols to UV-C light using a benchtop chamber equipped with a UVC exposure window. We evaluated virus susceptibility to UV-C doses ranging from 4 to 12 J/m
2
at three relative humidity levels (25, 50, and 75%). Our data show that the Z values (susceptibility factors) were higher (more susceptible) to UV-C than what has been reported previously. Furthermore, dose-response plots showed that influenza virus susceptibility increases with decreasing relative humidity. This work provides an essential scientific basis for designing and utilizing effective upper-room UV-C light installations for the prevention of the airborne transmission of influenza by characterizing its susceptibility to UV-C.
Characterization of Halomonas sp. Strain H11 α-Glucosidase Activated by Monovalent Cations and Its Application for Efficient Synthesis of α-
d
-Glucosylglycerol
Authors: Ojima Teruyo , Saburi Wataru , Yamamoto Takeshi , Kudo Toshiaki 
Published: January 2012

ABSTRACT

An α-glucosidase (HaG) with the following unique properties was isolated from
Halomonas
sp. strain H11: (i) high transglucosylation activity, (ii) activation by monovalent cations, and (iii) very narrow substrate specificity. The molecular mass of the purified HaG was estimated to be 58 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). HaG showed high hydrolytic activities toward maltose, sucrose, and
p
-nitrophenyl α-
d
-glucoside (
p
NPG) but to almost no other disaccharides or malto-oligosaccharides higher than trisaccharides. HaG showed optimum activity to maltose at 30°C and pH 6.5. Monovalent cations such as K
+
, Rb
+
, Cs
+
, and NH
4
+
increased the enzymatic activity to 2- to 9-fold of the original activity. These ions shifted the activity-pH profile to the alkaline side. The optimum temperature rose to 40°C in the presence of 10 mM NH
4
+
, although temperature stability was not affected. The apparent

K
m

and
k
cat
values for maltose and
p
NPG were significantly improved by monovalent cations. Surprisingly,
k
cat
/

K
m

for
p
NPG increased 372- to 969-fold in their presence. HaG used some alcohols as acceptor substrates in transglucosylation and was useful for efficient synthesis of α-
d
-glucosylglycerol. The efficiency of the production level was superior to that of the previously reported enzyme
Aspergillus niger
α-glucosidase in terms of small amounts of by-products. Sequence analysis of HaG revealed that it was classified in glycoside hydrolase family 13. Its amino acid sequence showed high identities, 60%, 58%, 57%, and 56%, to
Xanthomonas campestris
WU-9701 α-glucosidase,
Xanthomonas campestris
pv. raphani 756C oligo-1,6-glucosidase,
Pseudomonas stutzeri
DSM 4166 oligo-1,6-glucosidase, and
Agrobacterium tumefaciens
F2 α-glucosidase, respectively.
The Ubiquitin Ligase Ubr11 Is Essential for Oligopeptide Utilization in the Fission Yeast Schizosaccharomyces pombe
Authors: Kitamura Kenji , Nakase Mai , Tohda Hideki , Takegawa Kaoru 
Published: January 2012

ABSTRACT

Uptake of extracellular oligopeptides in yeast is mediated mainly by specific transporters of the peptide transporter (PTR) and oligopeptide transporter (OPT) families. Here, we investigated the role of potential peptide transporters in the yeast
Schizosaccharomyces pombe
. Utilization of naturally occurring dipeptides required only Ptr2/SPBC13A2.04c and none of the other 3 OPT proteins (Isp4, Pgt1, and Opt3), whereas only Isp4 was indispensable for tetrapeptide utilization. Both Ptr2 and Isp4 localized to the cell surface, but under rich nutrient conditions Isp4 localized in the Golgi apparatus through the function of the ubiquitin ligase Pub1. Furthermore, the ubiquitin ligase Ubr11 played a significant role in oligopeptide utilization. The mRNA levels of both the
ptr2
and
isp4
genes were significantly reduced in
ubr11
Δ cells, and the dipeptide utilization defect in the
ubr11
Δ mutant was rescued by the forced expression of Ptr2. Consistent with its role in transcriptional regulation of peptide transporter genes, the Ubr11 protein was accumulated in the nucleus. Unlike the situation in
Saccharomyces cerevisiae
, the oligopeptide utilization defect in the
S. pombe
ubr11
Δ mutant was not rescued by inactivation of the Tup11/12 transcriptional corepressors, suggesting that the requirement for the Ubr ubiquitin ligase in the upregulation of peptide transporter mRNA levels is conserved in both yeasts; however, the actual mechanism underlying the control appears to be different. We also found that the peptidomimetic proteasome inhibitor MG132 was still operative in a strain lacking all known PTR and OPT peptide transporters. Therefore, irrespective of its peptide-like structure, MG132 is carried into cells independently of the representative peptide transporters.
Roles of Long and Short Replication Initiation Proteins in the Fate of IncP-1 Plasmids
Authors: Yano Hirokazu , Deckert Gail E. , Rogers Linda M. , Top Eva M. 
Published: January 2012

ABSTRACTBroad-host-range IncP-1 plasmids generally encode two replication initiation proteins, TrfA1 and TrfA2. TrfA2 is produced from an internal translational start site withintrfA1. While TrfA1 was previously shown to be essential for replication inPseudomonas aeruginosa, its role in other bacteria within its broad host range has not been established. To address the role of TrfA1 and TrfA2 in other hosts, efficiency of transformation, plasmid copy number (PCN), and plasmid stability were first compared between a mini-IncP-1β plasmid and itstrfA1frameshift variant in four phylogenetically distant hosts:Escherichia coli,Pseudomonas putida,Sphingobium japonicum, andCupriavidus necator. TrfA2 was sufficient for replication in these hosts, but the presence of TrfA1 enhanced transformation efficiency and PCN. However, TrfA1 did not contribute to, and even negatively affected, long-term plasmid persistence. WhentrfAgenes were cloned under a constitutive promoter in the chromosomes of the four hosts, strains expressing either both TrfA1 and TrfA2 or TrfA1 alone, again, generally elicited a higher PCN of an IncP1-β replicon than strains expressing TrfA2 alone. When a single species of TrfA was produced at different concentrations inE. colicells, TrfA1 maintained a 3- to 4-fold higher PCN than TrfA2 at the same TrfA concentrations, indicating that replication mediated by TrfA1 is more efficient than that by TrfA2. These results suggest that the broad-host-range properties of IncP-1 plasmids are essentially conferred by TrfA2 and the intact replication origin alone but that TrfA1 is nonetheless important to efficiently establish plasmid replication upon transfer into a broad range of hosts.
Three-Dimensional Structures of Pathogenic and Saprophytic Leptospira Species Revealed by Cryo-Electron Tomography
Authors: Raddi Gianmarco , Morado Dustin R. , Yan Jie , Haake David A. , Yang X. Frank , Liu Jun 
Published: January 2012

ABSTRACTLeptospira interrogansis the primary causative agent of the most widespread zoonotic disease, leptospirosis. An in-depth structural characterization ofL. interrogansis needed to understand its biology and pathogenesis. In this study, cryo-electron tomography (cryo-ET) was used to compare pathogenic and saprophytic species and examine the unique morphological features of this group of bacteria. Specifically, our study revealed a structural difference between the cell envelopes ofL. interrogansandLeptospirabiflexainvolving variations in the lipopolysaccharide (LPS) layer. Through cryo-ET and subvolume averaging, we determined the first three-dimensional (3-D) structure of the flagellar motor of leptospira, with novel features in the flagellar C ring, export apparatus, and stator. Together with direct visualization of chemoreceptor arrays, DNA packing, periplasmic filaments, spherical cytoplasmic bodies, and a unique “cap” at the cell end, this report provides structural insights into these fascinatingLeptospiraspecies.
Taxonomy of Astragalus robbinsii var. fernaldii (Fabaceae): molecular and morphological analyses support transfer to Astragalus eucosmus
Authors: Sokoloff Paul C. , Gillespie Lynn J. 
Published: January 2012

Astragalus robbinsii var. fernaldii , Fernald’s milkvetch, is a taxon of conservation concern currently due for reassessment of its provincial and federal conservation status. Restricted to a narrow region spanning Newfoundland and Labrador and Quebec, its taxonomic position with respect to two congeners, Astragalus eucosmus and Astragalus robbinsii var. minor , is poorly understood. To clarify the taxonomy of Fernald’s milkvetch, we studied variation in the ycf6–trnC and trnC–rpoB chloroplast DNA (cpDNA) spacers, generated amplified fragment length polymorphism (AFLP) genotypes, and conducted a morphometric analysis. Parsimony and Bayesian analysis of the cpDNA data distinguished A. robbinsii var. minor from A. eucosmus and the majority of Fernald's milkvetch samples; both cpDNA and AFLP analysis were highly suggestive of gene flow between taxa and populations. Morphometric analysis indicates that Fernald's milkvetch is closer to A. eucosmus than to A. robbinsii var. minor in overall form and stipe length, while pubescence was not taxonomically informative. Based on these results, the recognition of Fernald's milkvetch is unwarranted; we recommend that the taxon be transferred to A. eucosmus.