bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new loss‐of‐function allele 28y reveals a role of ARGONAUTE1 in limiting asymmetric division of stomatal lineage ground cell
Authors: Yang Kezhen , Jiang Min , Le Jie 
Published: January 2014

AbstractIn Arabidopsis thaliana L., stomata are produced through a series of divisions including asymmetric and symmetric divisions. Asymmetric entry division of meristemoid mother cell produces two daughter cells, the smaller meristemoid and the larger sister cell, a stomatal lineage ground cell (SLGC). Stomatal lineage ground cells can differentiate into epidermal pavement cells but have the potential to divide asymmetrically, spacing divisions, to create satellite meristemoids. Peptide ligands and TOO MANY MOUTHS (TMM) and ERECTA family receptors regulate the initiation of stomatal lineages, activity, and orientation of spacing divisions. Here, we reported that a natural mutant 28y displayed an increased stomatal density and index. Using map‐based cloning, we identified mutation in ARGONAUTE1 (AGO1) as the cause of 28y phenotypes. Time‐lapse tracing of stomatal lineage cells reveals that stomatal overproduction in 28y is caused by the excessive asymmetric spacing division of SLGCs. Further genetic results demonstrated that AGO1 acts downstream of TMM and negatively regulates the SPCH transcripts, but in a brassinosteroid‐independent manner. Upregulation of AGAMOUS‐LIKE16 (AGL16) in 28y mutants suggests that AGO1 is required to restrict AGL16‐mediated stomatal spacing divisions, an miRNA pathway in addition to ligand‐receptor signaling modules.
Signaling events during initiation of arbuscular mycorrhizal symbiosis
Authors: Schmitz Alexa M. , Harrison Maria J. 
Published: January 2014

AbstractUnder nutrient‐limiting conditions, plants will enter into symbiosis with arbuscular mycorrhizal (AM) fungi for the enhancement of mineral nutrient acquisition from the surrounding soil. AM fungi live in close, intracellular association with plant roots where they transfer phosphate and nitrogen to the plant in exchange for carbon. They are obligate fungi, relying on their host as their only carbon source. Much has been discovered in the last decade concerning the signaling events during initiation of the AM symbiosis, including the identification of signaling molecules generated by both partners. This signaling occurs through symbiosis‐specific gene products in the host plant, which are indispensable for normal AM development. At the same time, plants have adapted complex mechanisms for avoiding infection by pathogenic fungi, including an innate immune response to general microbial molecules, such as chitin present in fungal cell walls. How it is that AM fungal colonization is maintained without eliciting a defensive response from the host is still uncertain. In this review, we present a summary of the molecular signals and their elicited responses during initiation of the AM symbiosis, including plant immune responses and their suppression.
Nitrate regulates rhizobial and mycorrhizal symbiosis in common bean (Phaseolus vulgaris L.)
Authors: Nanjareddy Kalpana , Blanco Lourdes , Arthikala Manoj‐Kumar , Affantrange Xochitl Alvarado , Sánchez Federico , Lara Miguel 
Published: January 2014

AbstractNitrogen‐limited conditions are considered to be a prerequisite for legume‐rhizobial symbiosis, but the effects of nitrate‐rich conditions on symbiotic status remain poorly understood. We addressed this issue by examining rhizobial (Rhizobim tropici) and arbusclar mycorrhizal (Glomus intraradices) symbiosis in Phaseolus vulgaris L. cv. Negro Jamapa under nitrate pre‐incubation and continuous nitrate conditions. Our results indicate that nitrate pre‐incubation, independent of the concentration, did not affect nodule development. However, the continuous supply of nitrate at high concentrations impaired nodule maturation and nodule numbers. Low nitrate conditions, in addition to positively regulating nodule number, biomass, and nitrogenase activity, also extended the span of nitrogen‐fixing activity. By contrast, for arbuscular mycorrhizae, continuous 10 and 50 mmol/L nitrate increased the percent root length colonization, concomitantly reduced arbuscule size, and enhanced ammonia transport without affecting phosphate transport. Therefore, in this manuscript, we have proposed the importance of nitrate as a positive regulator in promoting both rhizobial and mycorrhizal symbiosis in the common bean.
Source and genesis of sulphate and phosphate–sulphate minerals in a quartz‐sandstone cave environment
Authors: Sauro Francesco , Tisato Nicola , De Waele Jo , Bernasconi Stefano M. , Bontognali Tomaso R. R. , Galli Ermanno 
Published: January 2014

AbstractGypsum (CaSO4·2H2O), alunite (KAl3(SO4)2(OH)6), and rare phosphate–sulphate sanjuanite Al2(PO4)(SO4)(OH) 9(H2O) and rossiantonite (Al3(PO4)(SO4) 2(OH)2(H2O)14) have recently been identified as secondary mineral deposits in different quartz‐sandstone caves in the Gran Sabana region, Venezuela. Due to the extended time scale required for speleogenesis in the hard and barely soluble quartz‐sandstone lithology, these caves are considered to be as old as 20 to 30 My. The study of these peculiar secondary mineral deposits potentially reveals important insights for understanding the interaction between deep, superficial and atmospheric processes over thousands to perhaps millions of years. In this study, chemical and petrographic analyses of potential host rock sources, sulphur and oxygen isotope ratios, and meteorological, hydrological and geographical data are used to investigate the origin of sulphates and phospho–sulphates. The results suggest that the deposition of sulphates in these caves is not linked to the quartz‐sandstone host rock. Rather, these mineral deposits originate from an external atmospheric sulphate source, with potential contributions of marine non‐sea salt sulphates, terrestrial dimethyl sulphide and microbially reduced H2S from the forests or peatbogs within the watershed. Air currents within the caves are the most plausible means of transport for aerosols, driving the accumulation of sulphates and other secondary minerals in specific locations. Moreover, the studied sulphate minerals often co‐occur with silica speleothems of biological origin. Although this association would suggest a possible biogenic origin for the sulphates as well, direct evidence proving that microbes are involved in their formation is absent. Nonetheless, this study demonstrates that these quartz‐sandstone caves accumulate and preserve allogenic sulphates, playing a yet unrecognized role in the sulphur cycle of tropical environments.
Darkness and gulliver2/phyB mutation decrease the abundance of phosphorylated BZR1 to activate brassinosteroid signaling in Arabidopsis
Authors: Kim Bokyung , Jeong Yu Jeong , Corvalán Claudia , Fujioka Shozo , Cho Seoae , Park Taesung , Choe Sunghwa 
Published: January 2014

SummaryLight is essential for plant survival; as such, plants flexibly adjust their growth and development to best harvest light energy. Brassinosteroids (BRs), plant growth‐promoting steroid hormones, are essential for this plasticity of development. However, the precise mechanisms underlying BR‐mediated growth under different light conditions remain largely unknown. Here, we show that darkness increases the activity of the BR‐specific transcription factor, BZR1, by decreasing the phosphorylated (inactive) form of BZR1 in a proteasome‐dependent manner. We observed that COP1, a dark‐activated ubiquitin ligase, captures and degrades the inactive form of BZR1. In support of this, BZR1 is abundant in the cop1‐4 mutant. The removal of phosphorylated BZR1 in darkness increases the ratio of dephosphorylated to phosphorylated forms of BZR1, thus increasing the chance of active homodimers forming between dephosphorylated BZR1 proteins. Furthermore, a transcriptome analysis revealed the identity of genes that are likely to contribute to the differential growth of hypocotyls in light conditions. Transgenic misexpression of three genes under the 35S promoter in light conditions resulted in elongated petioles and hypocotyls. Our results suggest that light conditions directly control BR signaling by modulating BZR1 stability, and consequently by establishing light‐dependent patterns of hypocotyl growth in Arabidopsis.
Effect of phosphate‐based seed priming on strigolactone production and Striga hermonthica infection in cereals
Authors: Jamil M , Charnikhova T , Verstappen F , Ali Z , Wainwright H , Bouwmeester H J 
Published: January 2014

SummaryStrigolactones, plant‐secreted underground signalling molecules, play an important role in agricultural ecosystems, because they mediate the interaction of crops with symbiotic AM fungi and parasitic weeds like Striga hermonthica. Cereal host plants secret these signalling molecules particularly under nutrient‐deficient conditions and especially when phosphate (P) is limiting. The objective of the present study was to see the potential of P seed priming for S. hermonthica management in cereals in relation to strigolactone production. It has been demonstrated that P fertiliser application down‐regulates the production of these signalling molecules in the rhizosphere, which results in lower S. hermonthica infection of cereals. The laboratory study showed maximum production of strigolactones from dry and water‐soaked seeds, while seed soaking in P solution reduced their production. Similarly, maximum S. hermonthica infection was observed under control treatments with dry sowing or water soaking, while P seed soaking decreased S. hermonthica germination, emergence and dry biomass in all cereal crops. Our study shows that P seed priming resulted in lower exudation of strigolactones, which induced less S. hermonthica seeds germination and hence may lead to lower S. hermonthica infection. P‐based seed priming could prove to be an effective and affordable strategy to reduce S. hermonthica infection in cereals. Further research for practical field application is needed.
Distribution, Diversity, and Activities of Sulfur Dioxygenases in Heterotrophic Bacteria
Authors: Liu Honglei , Xin Yufeng , Xun Luying 
Published: January 2014

ABSTRACT

Sulfur oxidation by chemolithotrophic bacteria is well known; however, sulfur oxidation by heterotrophic bacteria is often ignored. Sulfur dioxygenases (SDOs) (EC 1.13.11.18) were originally found in the cell extracts of some chemolithotrophic bacteria as glutathione (GSH)-dependent sulfur dioxygenases. GSH spontaneously reacts with elemental sulfur to generate glutathione persulfide (GSSH), and SDOs oxidize GSSH to sulfite and GSH. However, SDOs have not been characterized for bacteria, including chemolithotrophs. The gene coding for human SDO (human ETHE1 [hETHE1]) in mitochondria was discovered because its mutations lead to a hereditary human disease, ethylmalonic encephalopathy. Using sequence analysis and activity assays, we discovered three subgroups of bacterial SDOs in the proteobacteria and cyanobacteria. Ten selected SDO genes were cloned and expressed in
Escherichia coli
, and the recombinant proteins were purified. The SDOs used Fe
2+
for catalysis and displayed considerable variations in specific activities. The wide distribution of SDO genes reveals the likely source of the hETHE1 gene and highlights the potential of sulfur oxidation by heterotrophic bacteria.
Watershed-Scale Fungal Community Characterization along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate
Authors: Jasrotia Puja , Green Stefan J. , Canion Andy , Overholt Will A. , Prakash Om , Wafula Denis , Hubbard Daniela , Watson David B. , Schadt Christopher W. , Brooks Scott C. , Kostka Joel E. 
Published: January 2014

ABSTRACT

The objective of this study was to characterize fungal communities in a subsurface environment cocontaminated with uranium and nitrate at the watershed scale and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution, and diversity of fungi in subsurface groundwater samples were determined using quantitative and semiquantitative molecular techniques, including quantitative PCR of eukaryotic small-subunit rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from the subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylum
Ascomycota
, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH <4.5) conditions. Fungal isolates recovered from subsurface sediments, including cultures of the genus
Coniochaeta
, which were detected in abundance in pyrosequence libraries of site groundwater samples, were shown to reduce nitrate to nitrous oxide. Denitrifying fungal isolates recovered from the site were classified and found to be distributed broadly within the phylum
Ascomycota
and within a single genus of the
Basidiomycota
. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under
in situ
acidic pH conditions.
Cas9-Based Tools for Targeted Genome Editing and Transcriptional Control
Authors: Xu Tao , Li Yongchao , Van Nostrand Joy D. , He Zhili , Zhou Jizhong 
Published: January 2014

ABSTRACT
Development of tools for targeted genome editing and regulation of gene expression has significantly expanded our ability to elucidate the mechanisms of interesting biological phenomena and to engineer desirable biological systems. Recent rapid progress in the study of a clustered, regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) protein system in bacteria has facilitated the development of newly facile and programmable platforms for genome editing and transcriptional control in a sequence-specific manner. The core RNA-guided Cas9 endonuclease in the type II CRISPR system has been harnessed to realize gene mutation and DNA deletion and insertion, as well as transcriptional activation and repression, with multiplex targeting ability, just by customizing 20-nucleotide RNA components. Here we describe the molecular basis of the type II CRISPR/Cas system and summarize applications and factors affecting its utilization in model organisms. We also discuss the advantages and disadvantages of Cas9-based tools in comparison with widely used customizable tools, such as Zinc finger nucleases and transcription activator-like effector nucleases.
Development of an Enzyme-Linked Immunosorbent Spot Assay To Measure Serum-Neutralizing Antibodies against Coxsackievirus B3
Authors: Yang Lisheng , He Delei , Tang Min , Li Zhiqun , Liu Che , Xu Longfa , Chen Yixin , Du Hailian , Zhao Qinjian , Zhang Jun , Cheng Tong , Xia Ningshao 
Published: January 2014

ABSTRACTCoxsackievirus B3 (CVB3) is the most common pathogen that induces acute and chronic viral myocarditis in children. The cytopathic effect (CPE)-based neutralization test (Nt-CPE) and the plaque reduction neutralization test (PRNT) are the most common methods for measuring neutralizing antibody titers against CVB3 in blood serum samples. However, these two methods are inefficient for CVB3 vaccine clinical trials, which require the testing of a large number of serum specimens. In this study, we developed an efficient neutralization test based on the enzyme-linked immunospot (Nt-ELISPOT) assay for measuring CVB3-neutralizing antibodies. This modified ELISPOT assay was based on the use of a monoclonal antibody against the viral capsid protein VP1 to detect the cells that are infected with CVB3, which, after immunoperoxidase staining, are counted as spots using an automated ELISPOT analyzer. Using the modified ELISPOT assay, we characterized the infection kinetics of CVB3 and divided the infection process of CVB3 on a cluster of cells into four phases. The stability of the Nt-ELISPOT was then evaluated. We found that over a wide range of infectious doses (102to 106.5× 50% tissue culture infectious dose [TCID50] per well), the neutralizing titers of the sera were steady as long as they were tested during the log phase or the first half of the stationary phase of growth of the spots. We successfully shortened the testing period from 7 days to approximately 20 h. We also found that there was a good correlation (R2= 0.9462) between the Nt-ELISPOT and the Nt-CPE assays. Overall, the Nt-ELISPOT assay is a reliable and efficient method for measuring neutralizing antibodies in serum.
Key Role of Effector Memory CD4+T Lymphocytes in a Short-Incubation Heparin-Binding Hemagglutinin Gamma Interferon Release Assay for the Detection of Latent Tuberculosis
Authors: Wyndham-Thomas Chloé , Corbière Véronique , Dirix Violette , Smits Kaatje , Domont Fanny , Libin Myriam , Loyens Marc , Locht Camille , Mascart Françoise 
Published: January 2014

ABSTRACTThe treatment of latent tuberculosis infection (LTBI) in target populations is one of the current WHO strategies for preventing active tuberculosis (TB) infection and reducing theMycobacterium tuberculosisreservoir. Therefore, powerful LTBI screening tools are indispensable. A gamma interferon release assay (IGRA) in response to the stimulation of peripheral blood mononuclear cells by the latency antigen native heparin-binding hemagglutinin (nHBHA-IGRA) has proven its potential for this purpose. We have evaluated its possible optimization through a reduction of incubation time from 96 to 24 h, while compensating for this by adding interleukin 7 (IL-7) to the medium. We have also investigated the phenotypes of the gamma interferon (IFN-γ)-producing cells after both short and long incubation times. One hundred thirty-one nonimmunocompromised patients were recruited from 3 Brussels-based university hospitals. They were divided into 1 of 4 subgroups according to theirM. tuberculosisinfection status (LTBI, TB infection, undeterminedM. tuberculosisinfection status, and noninfected controls). The novel 24-h nHBHA-IGRA was performed for all subjects, and a simultaneous 96-h classical HBHA-IGRA was performed for 79 individuals. The results showed a good correlation between the two tests, and the novel 24-h nHBHA-IGRA maintained the principal advantages of the classical test, namely, a high specificity for LTBI diagnosis, an absence of interference ofMycobacterium bovisBCG vaccination during infancy, and a relative discrimination between LTBI and TB infection. Whereas the commercialized IGRAs show a greater sensitivity for recent than for remoteM. tuberculosisinfections, the 24-h nHBHA-IGRA appears to have comparable diagnostic powers for recent and remote LTBI. The IFN-γ detected by the 24-h nHBHA-IGRA was mainly secreted by effector memory CD4+T lymphocytes, a finding suggestive of continuous HBHA presentation during latency.
Gamma Interferon Immunospot Assay of Pleural Effusion Mononuclear Cells for Diagnosis of Tuberculous Pleurisy
Authors: Liao Mingfeng , Yang Qianting , Zhang Jieyun , Zhang Mingxia , Deng Qunyi , Liu Haiying , Graner Michael W. , Kornfeld Hardy , Zhou Boping , Chen Xinchun 
Published: January 2014

ABSTRACTDiagnosis of tuberculous pleurisy remains a challenge in the clinic. In this study, we evaluated the usefulness of a previously developedMycobacterium tuberculosisantigen-specific gamma interferon enzyme-linked immunospot (ELISPOT) assay in the diagnosis of tuberculous pleurisy by testing a cohort of 352 patients with pleural effusion. We found thatM. tuberculosisantigen-specific gamma interferon-producing cells were enriched four to five times in pleural fluid compared with their levels in peripheral blood from patients with tuberuclous pleurisy assayed in parallel. The sensitivity, specificity, positive predictive value, and negative predictive value of the pleural fluid mononuclear cell ELISPOT assay for the diagnosis of tuberculous pleurisy were 95.7%, 100%, 100%, and 81.0%, respectively. In comparison, the sensitivity and specificity of the ELISPOT assay using peripheral blood mononuclear cells were 78.3% and 86.3%, respectively. The sensitivity and specificity of the pleural fluid adenosine deaminase activity test were 55.5% and 86.3%, respectively. These results demonstrate that theM. tuberculosisantigen-specific ELISPOT assay performed on pleural fluid mononuclear cells provides an accurate, rapid diagnosis of tuberculous pleurisy.
High-Throughput Assay Optimization and Statistical Interpolation of Rubella-Specific Neutralizing Antibody Titers
Authors: Lambert Nathaniel D. , Pankratz V. Shane , Larrabee Beth R. , Ogee-Nwankwo Adaeze , Chen Min-hsin , Icenogle Joseph P. , Poland Gregory A. 
Published: January 2014

ABSTRACTRubella remains a social and economic burden due to the high incidence of congenital rubella syndrome (CRS) in some countries. For this reason, an accurate and efficient high-throughput measure of antibody response to vaccination is an important tool. In order to measure rubella-specific neutralizing antibodies in a large cohort of vaccinated individuals, a high-throughput immunocolorimetric system was developed. Statistical interpolation models were applied to the resulting titers to refine quantitative estimates of neutralizing antibody titers relative to the assayed neutralizing antibody dilutions. This assay, including the statistical methods developed, can be used to assess the neutralizing humoral immune response to rubella virus and may be adaptable for assessing the response to other viral vaccines and infectious agents.
Topical CpG Adjuvantation of a Protein-Based Vaccine Induces Protective Immunity to Listeria monocytogenes
Authors: Cheng Wing Ki , Wee Kathleen , Kollmann Tobias R. , Dutz Jan P. 
Published: January 2014

ABSTRACTRobust CD8+T cell responses are essential for immune protection against intracellular pathogens. Using parenteral administration of ovalbumin (OVA) protein as a model antigen, the effect of the Toll-like receptor 9 (TLR9) agonist, CpG oligodeoxynucleotide (ODN) 1826, as an adjuvant delivered either topically, subcutaneously, or intramuscularly on antigen-specific CD8+T cell responses in a mouse model was evaluated. Topical CpG adjuvant increased the frequency of OVA-specific CD8+T cells in the peripheral blood and in the spleen. The more effective strategy to administer topical CpG adjuvant to enhance CD8+T cell responses was single-dose administration at the time of antigen injection with a prime-boost regimen. Topical CpG adjuvant conferred both rapid and long-lasting protection against systemic challenge with recombinantListeria monocytogenesexpressing the cytotoxic T lymphocyte (CTL) epitope of OVA257–264(strainLm-OVA) in a TLR9-dependent manner. Topical CpG adjuvant induced a higher proportion of CD8+effector memory T cells than parenteral administration of the adjuvant. Although traditional vaccination strategies involve coformulation of antigen and adjuvant, split administration using topical adjuvant is effective and has advantages of safety and flexibility. Split administration of topical CpG ODN 1826 with parenteral protein antigen is superior to other administration strategies in enhancing both acute and memory protective CD8+T cell immune responses to subcutaneous protein vaccines. This vaccination strategy induces rapid and persistent protective immune responses against the intracellular organismL. monocytogenes.