bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation and characterization of 27 microsatellite markers for the endemic species Diplarche multiflora (Ericaceae)
Authors: Zhang Lin , Zhang Zhi‐Rong , Gao Lian‐Ming 
Published: March 2013

• Premise of the study: Microsatellite markers from the genome of Diplarche multiflora were developed and characterized to investigate its genetic diversity and population structure.• Methods and Results: Twenty‐seven microsatellite loci were isolated from the genome of D. multiflora using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol. Of these markers, 17 were polymorphic, and the number of alleles for the polymorphic microsatellite markers ranged from two to four, with an average of 2.2 per allele. The observed and expected heterozygosities varied from 0.0000 to 1.0000 and from 0.0000 to 0.7826, respectively.• Conclusions: These polymorphic microsatellite markers will be useful for population genetic studies and for assessing the genetic diversity of this alpine species.
Enhancing PCR amplification of DNA from recalcitrant plant specimens using a trehalose‐based additive
Authors: Samarakoon Tharangamala , Wang Shiao Y. , Alford Mac H. 
Published: March 2013

• Premise of the study: PCR amplification of DNA extracted from plants is sometimes difficult due to the presence of inhibitory compounds. An effective method to overcome the inhibitory effect of compounds that contaminate DNA from difficult plant specimens is needed.• Methods and Results: The effectiveness of a PCR additive reagent containing trehalose, bovine serum albumin (BSA), and polysorbate‐20 (Tween‐20) (TBT‐PAR) was tested. PCR of DNA extracted from fresh, silica‐dried, and herbarium leaf material of species of Achariaceae, Asteraceae, Lacistemataceae, and Samydaceae that failed using standard techniques were successful with the addition of TBT‐PAR.• Conclusions: The addition of TBT‐PAR during routine PCR is an effective method to improve amplification of DNA extracted from herbarium specimens or plants that are known to contain PCR inhibitors.
Isolation and characterization of microsatellite markers for the cleistogamous species Lamium amplexicaule (Lamiaceae)
Authors: Stojanova Bojana , Dubois Marie‐Pierre , Maurice Sandrine , Cheptou Pierre‐Olivier 
Published: March 2013

• Premise of the study: Lamium amplexicaule is a cleistogamous plant that produces both closed flowers (obligately self‐pollinated) and open flowers (potentially outcrossed). The conditions for the maintenance of such a mating system depend on the outcrossing rate of the open flowers, which can be estimated using neutral microsatellite markers.• Methods and Results: Forty primer pairs corresponding to microsatellite motifs obtained by coupling multiplex microsatellite enrichment and next‐generation sequencing were tested. Thirteen primers amplified with satisfying results. The polymorphism of these markers was studied in four French populations. Allele number varied from one to eight per locus and per population. Heterozygosity levels were significantly lower than those expected under Hardy–Weinberg equilibrium.• Conclusions: Our results are consistent with a partial self‐fertilization pattern. These markers will be used to estimate the outcrossing rate as well as population differentiation in L. amplexicaule.
Development and characterization of polymorphic microsatellite loci in Phellodendron amurense (Rutaceae)
Authors: Yu Jing‐Hua , Chen Chang‐Mei , Han Shi‐Jie , Guo Xiao‐Rui , Yuan Shu‐Sheng , Wang Chun‐Jing , Zu Yuan‐Gang 
Published: March 2013

• Premise of the study: Microsatellite markers were developed for the rare species Phellodendron amurense to assess the genetic diversity and population structure of this plant.• Methods and Results: In total, 27 microsatellite markers were developed for P. amurense by using an enriched genomic library and hybridization; all of these primers successfully amplified DNA fragments in P. amurense. These markers were screened in 74 individuals from four populations in China; 15 loci were found to be polymorphic, with the number of alleles per locus ranging from one to nine.• Conclusions: The microsatellite markers developed here represent a useful tool for studying the population genetic structure of P. amurense and to inform toward the development of effective conservation programs for this species.
A clearing protocol for whole tissues: An example using haustoria of Orobanchaceae
Authors: Morawetz Jeffery J. 
Published: March 2013

• Premise of the study: Due to lack of success in clearing whole tissues using only classical clearing techniques (e.g., Herr's 4½ solution, KOH, NaOH, lactic acid saturated with chloral hydrate), and because tissue degradation is often a result of harsh clearing agents (e.g., KOH, NaOH), a novel combined treatment was sought to improve the removal of obscuring tannins from intact haustoria.• Methods and Results: Stockwell's bleach proved to be useful in removing tannins from haustoria, usually within 3 d (up to 10 d), rendering them opaque to (rarely) translucent. After bleaching, haustoria were successfully cleared in 1–3 d in a solution of lactic acid saturated with chloral hydrate at 42°C.• Conclusions: The two‐step clearing protocol reported here will now facilitate structural studies on haustoria, such as those examining the presence and distribution of callose, and three‐dimensional reconstruction using confocal microscopy. Tissues in this study did not suffer from the degradation in quality observed using harsher treatments. This protocol should be useful for other difficult‐to‐clear tissues that are unable to be cleared using classical protocols alone.
Development of 32 EST‐SSR markers for Abies firma (Pinaceae) and their transferability to related species
Authors: Uchiyama Kentaro , Fujii Sayaka , Ishizuka Wataru , Goto Susumu , Tsumura Yoshihiko 
Published: March 2013

• Premise of the study: We developed simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) for Abies firma, a conifer endemic in Japan, to facilitate evaluation of the population genetic structure in this species.• Methods and Results: We designed primers for 153 EST‐SSRs identified from 486322 ESTs from A. sachalinensis ESTs, and tested 96 of them for PCR amplification. Thirty‐two primers provided clear amplification, and 14 of those 32 displayed clear polymorphic patterns in multiple populations of A. firma and in two closely related species. The number of alleles per locus and mean expected heterozygosity ranged from one to six and 0 to 0.476, respectively.• Conclusions: The EST‐SSR markers developed in this study may be useful for phylogeography and population genetic studies of A. firma. Successful amplifications were obtained for two other Abies species, suggesting that these markers may also be useful for similar applications in other fir species.
A targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes
Authors: Stull Gregory W. , Moore Michael J. , Mandala Venkata S. , Douglas Norman A. , Kates Heather‐Rose , Qi Xinshuai , Brockington Samuel F. , Soltis Pamela S. , Soltis Douglas E. , Gitzendanner Matthew A. 
Published: March 2013

• Premise of the study: We explored a targeted enrichment strategy to facilitate rapid and low‐cost next‐generation sequencing (NGS) of numerous complete plastid genomes from across the phylogenetic breadth of angiosperms.• Methods and Results: A custom RNA probe set including the complete sequences of 22 previously sequenced eudicot plastomes was designed to facilitate hybridization‐based targeted enrichment of eudicot plastid genomes. Using this probe set and an Agilent SureSelect targeted enrichment kit, we conducted an enrichment experiment including 24 angiosperms (22 eudicots, two monocots), which were subsequently sequenced on a single lane of the Illumina GAIIx with single‐end, 100‐bp reads. This approach yielded nearly complete to complete plastid genomes with exceptionally high coverage (mean coverage: 717×), even for the two monocots.• Conclusions: Our enrichment experiment was highly successful even though many aspects of the capture process employed were suboptimal. Hence, significant improvements to this methodology are feasible. With this general approach and probe set, it should be possible to sequence more than 300 essentially complete plastid genomes in a single Illumina GAIIx lane (achieving ∼50× mean coverage). However, given the complications of pooling numerous samples for multiplex sequencing and the limited number of barcodes (e.g., 96) available in commercial kits, we recommend 96 samples as a current practical maximum for multiplex plastome sequencing. This high‐throughput approach should facilitate large‐scale plastid genome sequencing at any level of phylogenetic diversity in angiosperms.
Engineered DNA polymerase improves PCR results for plastid DNA
Authors: Schori Melanie , Appel Maryke , Kitko AlexaRae , Showalter Allan M. 
Published: March 2013

• Premise of the study: Secondary metabolites often inhibit PCR and sequencing reactions in extractions from plant material, especially from silica‐dried and herbarium material. A DNA polymerase that is tolerant to inhibitors improves PCR results.• Methods and Results: A novel DNA amplification system, including a DNA polymerase engineered via directed evolution for improved tolerance to common plant‐derived PCR inhibitors, was evaluated and PCR parameters optimized for three species. An additional 31 species were then tested with the engineered enzyme and optimized protocol, as well as with regular Taq polymerase.• Conclusions: PCR products and high‐quality sequence data were obtained for 96% of samples for rbcL and 79% for matK, compared to 29% and 21% with regular Taq polymerase.
Euthanasie : vrai pouvoir sur soi donné aux vieux ou simple angoisse des jeunes devant la douleur ?
Authors: Quentin Bertrand 
Published: March 2013

Le débat actuel en France autour de la question de l’euthanasie est révélateur de deux obsessions de la société occidentale contemporaine : une tendance à vouloir fuir toute douleur – ce que nous appelons l’« algophobie » ; et une tendance à magnifier la volonté individuelle au service de laquelle la société devrait en toute circonstance se plier. Nous verrons en quoi, dans ces questions, les jeunes s’écoutent souvent plus qu’ils n’écoutent réellement leurs vieux.
Viscosités pragmatiques
Authors: Bougnoux Daniel 
Published: March 2013

Le flot des innovations ou des marchandises nous pousse en avant pour trouver du nouveau ; cette course impitoyable a pourtant sa butée dans nos relations pragmatiques, qui valorisent un temps lent et long, et changent l’obstacle de l’archaïsme en gage de succès. L’effet jogging des médiologues demande à être explicité.
Functional Genetic Variation inNFKBIAand Susceptibility to Childhood Asthma, Bronchiolitis, and Bronchopulmonary Dysplasia
Authors: Ali Salman , Hirschfeld Aaron F. , Mayer Matthew L. , Fortuno Edgardo S. , Corbett Nathan , Kaplan Maia , Wang Shirley , Schneiderman Julia , Fjell Christopher D. , Yan Jin , Akhabir Loubna , Aminuddin Farzian , Marr Nico , Lacaze-Masmonteil Thierry , Hegele Richard G. , Becker Allan , Chan-Yeung Moira , Hancock Robert E. W. , Kollmann Tobias R. , Daley Denise , Sandford Andrew J. , Lavoie Pascal M. , Turvey Stuart E. 
Published: March 2013

AbstractRespiratory diseases are the most frequent chronic illnesses in babies and children. Although a vigorous innate immune system is critical for maintaining lung health, a balanced response is essential to minimize damaging inflammation. We investigated the functional and clinical impact of human genetic variants in the promoter of NFKBIA, which encodes IκBα, the major negative regulator of NF-κB. In this study, we quantified the functional impact of NFKBIA promoter polymorphisms (rs3138053, rs2233406, and rs2233409) on promoter-driven protein expression, allele-specific and total NFKBIA mRNA expression, IκBα protein expression, and TLR responsiveness; mapped innate immune regulatory networks active during respiratory syncytial virus infection, asthma, and bronchopulmonary dysplasia; and genotyped and analyzed independent cohorts of children with respiratory syncytial virus infection, asthma, and bronchopulmonary dysplasia. Genetic variants in the promoter of NFKBIA influenced NFKBIA gene expression, IκBα protein expression, and TLR-mediated inflammatory responses. Using a systems biology approach, we demonstrated that NFKBIA/IκBα is a central hub in transcriptional responses of prevalent childhood lung diseases, including respiratory syncytial virus infection, asthma, and bronchopulmonary dysplasia. Finally, by examining independent pediatric lung disease cohorts, we established that this immunologically relevant genetic variation in the promoter of NFKBIA is associated with differential susceptibility to severe bronchiolitis following infection with respiratory syncytial virus, airway hyperresponsiveness, and severe bronchopulmonary dysplasia. These data highlight the importance of negative innate immune regulators, such as NFKBIA, in pediatric lung disease and begin to unravel common aspects in the genetic predisposition to bronchopulmonary dysplasia, bronchiolitis, and childhood asthma.
Profibrotic Activities for Matrix Metalloproteinase-8 during Bleomycin-Mediated Lung Injury
Authors: Craig Vanessa J. , Quintero Pablo A. , Fyfe Susanne E. , Patel Avignat S. , Knolle Martin D. , Kobzik Lester , Owen Caroline A. 
Published: March 2013

Abstract
Matrix metalloproteinase-8 (MMP-8) is a potent interstitial collagenase thought to be expressed mainly by polymorphonuclear neutrophils. To determine whether MMP-8 regulates lung inflammatory or fibrotic responses to bleomycin, we delivered bleomycin by the intratracheal route to wild-type (WT) versus Mmp-8−/− mice and quantified MMP-8 expression, and inflammation and fibrosis in the lung samples. Mmp-8 steady state mRNA and protein levels increase in whole lung and bronchoalveolar lavage samples when WT mice are treated with bleomycin. Activated murine lung fibroblasts express Mmp-8 in vitro. MMP-8 expression is increased in leukocytes in the lungs of patients with idiopathic pulmonary fibrosis compared with control lung samples. Compared with bleomycin-treated WT mice, bleomycin-treated Mmp-8−/− mice have greater lung inflammation, but reduced lung fibrosis. Whereas bleomycin-treated Mmp-8−/− and WT mice have similar lung levels of several pro- and antifibrotic mediators (TGF-β, IL-13, JE, and IFN-γ), Mmp-8−/− mice have higher lung levels of IFN-γ–inducible protein-10 (IP-10) and MIP-1α. Genetically deleting either Ip-10 or Mip-1α in Mmp-8−/− mice abrogates their lung inflammatory response to bleomycin, but reconstitutes their lung fibrotic response to bleomycin. Studies of bleomycin-treated Mmp-8 bone marrow chimeric mice show that both leukocytes and lung parenchymal cells are sources of profibrotic MMP-8 during bleomycin-mediated lung fibrosis. Thus, during bleomycin-mediated lung injury, MMP-8 dampens the lung acute inflammatory response, but promotes lung fibrosis by reducing lung levels of IP-10 and MIP-1α. These data indicate therapeutic strategies to reduce lung levels of MMP-8 may limit fibroproliferative responses to injury in the human lung.
Bcl6 Expressing Follicular Helper CD4 T Cells Are Fate Committed Early and Have the Capacity To Form Memory
Authors: Choi Youn Soo , Yang Jessica A. , Yusuf Isharat , Johnston Robert J. , Greenbaum Jason , Peters Bjoern , Crotty Shane 
Published: March 2013

Abstract
Follicular helper CD4 T (Tfh) cells are a distinct type of differentiated CD4 T cells uniquely specialized for B cell help. In this study, we examined Tfh cell fate commitment, including distinguishing features of Tfh versus Th1 proliferation and survival. Using cell transfer approaches at early time points after an acute viral infection, we demonstrate that early Tfh cells and Th1 cells are already strongly cell fate committed by day 3. Nevertheless, Tfh cell proliferation was tightly regulated in a TCR-dependent manner. The Tfh cells still depend on extrinsic cell fate cues from B cells in their physiological in vivo environment. Unexpectedly, we found that Tfh cells share a number of phenotypic parallels with memory precursor CD8 T cells, including selective upregulation of IL-7Rα and a collection of coregulated genes. As a consequence, the early Tfh cells can progress to robustly form memory cells. These data support the hypothesis that CD4 and CD8 T cells share core aspects of a memory cell precursor gene expression program involving Bcl6, and a strong relationship exists between Tfh cells and memory CD4 T cell development.
Divergent Effects of T Cell Costimulation and Inflammatory Cytokine Production on Autoimmune Peripheral Neuropathy Provoked by Aire Deficiency
Authors: Zeng Xiaopei L. , Nagavalli Anil , Smith Colin-Jamal , Howard James F. , Su Maureen A. 
Published: March 2013

Abstract
Chronic inflammatory demyelinating polyneuropathy results from autoimmune destruction of the peripheral nervous system and is a component of the multiorgan autoimmunity syndrome that results from Aire gene mutations in humans. In parallel, peripheral nervous system autoimmunity resembling chronic inflammatory demyelinating polyneuropathy develops spontaneously in NOD mice with a partial loss of Aire function (NOD.AireGW/+ mice) and is a T cell–mediated disease. In this study, we analyze how key aspects of T cell activation and function modulate disease development in Aire-deficient mice. We show that genetic ablation of the Th1 cytokine IFN-γ completely prevents clinical and electrophysiological evidence of neuropathy in NOD.AireGW/+ mice. IFN-γ deficiency is associated with absence of immune infiltration and decreased expression of the T cell chemoattractant IP-10 in sciatic nerves. Thus, IFN-γ is absolutely required for the development of autoimmune peripheral neuropathy in NOD.AireGW/+ mice. Because IFN-γ secretion is enhanced by B7-CD28 costimulation of T cells, we sought to determine the effects of these costimulatory molecules on neuropathy development. Surprisingly, B7-2 deficiency accelerated neuropathy development in NOD.AireGW/+ mice, and Ab blockade of both B7-1 and B7-2 resulted in fulminant, early-onset neuropathy. Thus, in contrast to IFN-γ, B7-2 alone and B7-1/B7-2 in combination function to ameliorate neuropathy development in NOD.AireGW/+ mice. Together, these findings reveal distinct and opposing effects of the T cell costimulatory pathway and IFN-γ production on the pathogenesis of autoimmune peripheral neuropathy.
Liver Sinusoidal Endothelial Cell Lectin Inhibits CTL-Dependent Virus Clearance in Mouse Models of Viral Hepatitis
Authors: Liu Biao , Wang Min , Wang Xiaowen , Zhao Dianyuan , Liu Di , Liu Jing , Chen Pei-Jer , Yang Dongliang , He Fuchu , Tang Li 
Published: March 2013

Abstract
Liver sinusoidal endothelial cell lectin (LSECtin) was recently reported to suppress intrahepatic T cell immunity and to limit immune-mediated liver injury. However, its role in the outcome and pathogenesis of viral infection has not yet been elucidated. Using a mouse model infected with a hepatotropic adenovirus, we found that the absence of LSECtin led to a higher frequency of intrahepatic effector CTLs. These cells produced higher levels of antiviral cytokines and cytotoxic factors and exhibited an increased expression of the transcription factors T-bet and Runx3. This phenotype observed in the LSECtin-knockout cells mediated a more efficient virus-specific cytotoxity compared with that of wild-type cells. As a consequence, LSECtin deficiency significantly accelerated liver adenovirus clearance. In contrast, LSECtin upregulation in the liver delayed viral clearance; this delayed clearance was accompanied by the downregulation of the antiviral activity of CTLs. We further constructed an immunocompetent mouse model of acute hepatitis B viral infection to demonstrate that LSECtin significantly delayed the clearance of hepatitis B virus from blood and infected hepatocytes by limiting the frequency of hepatitis B virus–specific IFN-γ–producing cells. Consistent with this function, LSECtin was upregulated in the liver of mouse models of viral hepatitis. Taken together, our results suggest that LSECtin may facilitate the reduction of liver inflammation at the cost of delaying virus clearance and that this effect might be hijacked by the virus as an escape mechanism.
Fibrin Facilitates Both Innate and T Cell–Mediated Defense againstYersinia pestis
Authors: Luo Deyan , Lin Jr-Shiuan , Parent Michelle A. , Mullarky-Kanevsky Isis , Szaba Frank M. , Kummer Lawrence W. , Duso Debra K. , Tighe Michael , Hill Jim , Gruber Andras , Mackman Nigel , Gailani David , Smiley Stephen T. 
Published: March 2013

AbstractThe Gram-negative bacterium Yersinia pestis causes plague, a rapidly progressing and often fatal disease. The formation of fibrin at sites of Y. pestis infection supports innate host defense against plague, perhaps by providing a nondiffusible spatial cue that promotes the accumulation of inflammatory cells expressing fibrin-binding integrins. This report demonstrates that fibrin is an essential component of T cell–mediated defense against plague but can be dispensable for Ab-mediated defense. Genetic or pharmacologic depletion of fibrin abrogated innate and T cell–mediated defense in mice challenged intranasally with Y. pestis. The fibrin-deficient mice displayed reduced survival, increased bacterial burden, and exacerbated hemorrhagic pathology. They also showed fewer neutrophils within infected lung tissue and reduced neutrophil viability at sites of liver infection. Depletion of neutrophils from wild-type mice weakened T cell–mediated defense against plague. The data suggest that T cells combat plague in conjunction with neutrophils, which require help from fibrin to withstand Y. pestis encounters and effectively clear bacteria.
Participation in the Home Environment among Children and Youth with and without Disabilities
Authors: Law Mary , Anaby Dana , Teplicky Rachel , Khetani Mary Alunkal , Coster Wendy , Bedell Gary 
Published: March 2013

Introduction: This study examines participation patterns and environmental supports and barriers for children with and without disabilities within their home setting. Method: The Participation and Environment Measure for Children and Youth (PEM-CY) is a newly developed, reliable parent/caregiver-report tool, which combines assessment of children's participation and the environment. The PEM-CY was completed online by 576 parents of children or youth (5 to 17 years old) with and without disabilities from Canada and the United States. ANOVA analyses were performed to examine group differences in PEM-CY summary scores. Item-level differences are presented descriptively using radar plots. Results: After controlling for age and income, significant differences between children with and without disabilities were observed for all home-based PEM-CY participation and environment summary scores. Differences between the two groups were also evident at the item level, particularly when comparing the percentage of children and youth who never participate in specific home-based activities and when comparing perceived barriers to participation. Conclusion: Although all children and youth participate frequently in home-based activities, those with disabilities tend to participate in less complex and quieter/sedentary activities. This, in addition to parental report of environmental barriers to participation, highlights the potential importance of home-based occupational therapy intervention to optimise participation in this setting.