bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualizing metabolite distribution and enzymatic conversion in plant tissues by desorption electrospray ionization mass spectrometry imaging
Authors: Li Bin , Knudsen Camilla , Hansen Natascha Krahl , Jørgensen Kirsten , Kannangara Rubini , Bak Søren , Takos Adam , Rook Fred , Hansen Steen H. , Møller Birger Lindberg , Janfelt Christian , Bjarnholt Nanna 
Published: March 2013

SummaryIn comparison with the technology platforms developed to localize transcripts and proteins, imaging tools for visualization of metabolite distributions in plant tissues are less well developed and lack versatility. This hampers our understanding of plant metabolism and dynamics. In this study, we demonstrate that desorption electrospray ionization mass spectrometry imaging (DESI‐MSI) of tissue imprints on porous Teflon may be used to accurately image the distribution of even labile plant metabolites such as hydroxynitrile glucosides, which normally undergo enzymatic hydrolysis by specific β‐glucosidases upon cell disruption. This fast and simple sample preparation resulted in no substantial differences in the distribution and ratios of all hydroxynitrile glucosides between leaves from wild‐type Lotus japonicus and a β‐glucosidase mutant plant that lacks the ability to hydrolyze certain hydroxynitrile glucosides. In wild‐type, the enzymatic conversion of hydroxynitrile glucosides and the concomitant release of glucose were easily visualized when a restricted area of the leaf tissue was damaged prior to sample preparation. The gene encoding the first enzyme in hydroxynitrile glucoside biosynthesis in L. japonicus leaves, CYP79D3, was found to be highly expressed during the early stages of leaf development, and the hydroxynitrile glucoside distribution in mature leaves reflected this early expression pattern. The utility of direct DESI‐MSI of plant tissue was demonstrated using cryo‐sections of cassava (Manihot esculenta) tubers. The hydroxynitrile glucoside levels were highest in the outer cell layers, as verified by LC–MS analyses. The unexpected discovery of a hydroxynitrile‐derived di‐glycoside shows the potential of DESI‐MSI to discover and guide investigations into new metabolic routes.
PIN6 is required for nectary auxin response and short stamen development
Authors: Bender Ricci L. , Fekete Megan L. , Klinkenberg Peter M. , Hampton Marshall , Bauer Brittany , Malecha Matthew , Lindgren Khrystyne , A. Maki Jennifer , Perera M. Ann D. N. , Nikolau Basil J. , Carter Clay J. 
Published: March 2013

SummaryThe PIN family of proteins is best known for its involvement in polar auxin transport and tropic responses. PIN6 (At1g77110) is one of the remaining PIN family members in Arabidopsis thaliana to which a biological function has not yet been ascribed. Here we report that PIN6 is a nectary‐enriched gene whose expression level is positively correlated with total nectar production in Arabidopsis, and whose function is required for the proper development of short stamens. PIN6 accumulates in internal membranes consistent with the ER, and multiple lines of evidence demonstrate that PIN6 is required for auxin‐dependent responses in nectaries. Wild‐type plants expressing auxin‐responsive DR5:GFP or DR5:GUS reporters displayed intense signal in lateral nectaries, but pin6 lateral nectaries showed little or no signal for these reporters. Further, exogenous auxin treatment increased nectar production more than tenfold in wild‐type plants, but nectar production was not increased in pin6 mutants when treated with auxin. Conversely, the auxin transport inhibitor N–1–naphthylphthalamic acid (NPA) reduced nectar production in wild‐type plants by more than twofold, but had no significant effect on pin6 lines. Interestingly, a MYB57 transcription factor mutant, myb57–2, closely phenocopied the loss‐of‐function mutant pin6–2. However, PIN6 expression was not dependent on MYB57, and RNA‐seq analyses of pin6–2 and myb57–2 mutant nectaries showed little overlap in terms of differentially expressed genes. Cumulatively, these results demonstrate that PIN6 is required for proper auxin response and nectary function in Arabidopsis. These results also identify auxin as an important factor in the regulation of nectar production, and implicate short stamens in the maturation of lateral nectaries.
Cold shock protein 1 chaperones mRNAs during translation in Arabidopsis thaliana
Authors: Juntawong Piyada , Sorenson Reed , Bailey‐Serres Julia 
Published: March 2013

SummaryRNA binding proteins (RBPs) function post‐transcriptionally to fine‐tune gene regulation. Arabidopsis thaliana has four Gly‐rich, zinc finger‐containing RBPs called cold shock proteins 1–4 (CSP1–CSP4), that possess an evolutionary conserved cold shock domain. Here, we determined that CSP1 associates with polyribosomes (polysomes) via an RNA‐mediated interaction. Both the abundance and polysomal co‐fractionation of CSP1 was enhanced in the cold (4°C), but did not influence global levels of polysomes, which were minimally perturbed by above freezing cold temperatures. Using a polyclonal antiserum, CSP1 was co‐immunopurified with several hundred transcripts from rosettes of plants cultivated at 23°C or transferred to 4°C for 12 h. CSP1‐associated mRNAs were characterized by G+C‐rich 5′ untranslated regions and gene ontologies related to cellular respiration, mRNA binding and translation. The majority of the CSP1‐associated mRNAs were constitutively expressed and stable in the cold. CSP1 abundance was correlated with improved translation of ribosomal protein mRNAs during cold stress and improved maintenance of homeostasis and translation of mRNAs under water‐deficit stress. In summary, CSP1 selectively chaperones mRNAs, providing translational enhancement during stress.
Neutrophil activity in chronic venous leg ulcers—A target for therapy?
Authors: McDaniel Jodi C. , Roy Sashwati , Wilgus Traci A. 
Published: March 2013

AbstractChronic venous leg ulcers (CVLUs) affect approximately 600,000 people annually in the United States and accrue yearly treatment costs of US$2.5–5 billion. As the population ages, demands on health care resources for CVLU treatments are predicted to drastically increase because the incidence of CVLUs is highest in those ≥65 years of age. Furthermore, regardless of current standards of care, healing complications and high recurrence rates prevail. Thus, it is critical that factors leading to or exacerbating CVLUs be discerned and more effective, adjuvant, evidence‐based treatment strategies be utilized. Previous studies have suggested that CVLUs' pathogenesis is related to the prolonged presence of high numbers of activated neutrophils secreting proteases in the wound bed that destroy growth factors, receptors, and the extracellular matrix that are essential for healing. These events are believed to contribute to a chronically inflamed wound that fails to heal. Therefore, the purpose of this project was to review studies from the past 15 years (1996–2011) that characterized neutrophil activity in the microenvironment of human CVLUs for new evidence that could explicate the proposed relationship between excessive, sustained neutrophil activity and CVLUs. We also appraised the strength of evidence for current and potential therapeutics that target excessive neutrophil activity.
Lactobacillus rhamnosus Ingestion Promotes Innate Host Defense in an Enteric Parasitic Infection
Authors: McClemens Jessica , Kim Janice J. , Wang Huaqing , Mao Yu-Kang , Collins Matthew , Kunze Wolfgang , Bienenstock John , Forsythe Paul , Khan Waliul I. 
Published: March 2013

ABSTRACT

Enteric parasite infections around the world are a huge economic burden and decrease the quality of life for many people. The use of beneficial bacteria has attracted attention for their potential therapeutic applications in various diseases. However, the effects of beneficial bacteria in enteric parasitic infections remain largely unexplored. We investigated the effects of ingestion of
Lactobacillus rhamnosus
(JB-1) in a model of enteric nematode (
Trichuris muris
) infection. C57BL/6 (resistant to infection), AKR (susceptible to infection), interleukin 10 (IL-10) knockout (KO), and mucin Muc2 KO mice were infected with
T. muris
and treated orally with probiotic JB-1 or medium. The mice were sacrificed on various days postinfection to examine goblet cells, epithelial cell proliferation, cytokines, and worm burdens. Treatment with JB-1 significantly enhanced worm expulsion in resistant C57BL/6 mice, and this was associated with increases in IL-10 levels, goblet cell numbers, and epithelial cell proliferation. Beneficial effects of JB-1 were absent in IL-10 KO and resistant mice treated with γ-irradiated bacteria. Live JB-1 treatment also expedited worm expulsion in Muc2 KO mice and, more importantly, in AKR mice (susceptible to infection). Injection of IL-10 directly into the colonic tissue of uninfected mice induced goblet cell hyperplasia. These findings demonstrate that JB-1 modulates goblet cell biology and promotes parasite expulsion via an IL-10-mediated pathway and provide novel insights into probiotic effects on innate defense in nematode infection.
Transgenic Parasites Stably Expressing Full-Length Plasmodium falciparum Circumsporozoite Protein as a Model for Vaccine Down-Selection in Mice Using Sterile Protection as an Endpoint
Authors: Porter Michael D. , Nicki Jennifer , Pool Christopher D. , DeBot Margot , Illam Ratish M. , Brando Clara , Bozick Brooke , De La Vega Patricia , Angra Divya , Spaccapelo Roberta , Crisanti Andrea , Murphy Jittawadee R. , Bennett Jason W. , Schwenk Robert J. , Ockenhouse Christian F. , Dutta Sheetij 
Published: March 2013

ABSTRACTCircumsporozoite protein (CSP) ofPlasmodium falciparumis a protective human malaria vaccine candidate. There is an urgent need for models that can rapidly down-select novel CSP-based vaccine candidates. In the present study, the mouse-mosquito transmission cycle of a transgenicPlasmodium bergheimalaria parasite stably expressing a functional full-lengthP. falciparumCSP was optimized to consistently produce infective sporozoites for protection studies. A minimal sporozoite challenge dose was established, and protection was defined as the absence of blood-stage parasites 14 days after intravenous challenge. The specificity of protection was confirmed by vaccinating mice with multiple CSP constructs of differing lengths and compositions. Constructs that induced high NANP repeat-specific antibody titers in enzyme-linked immunosorbent assays were protective, and the degree of protection was dependent on the antigen dose. There was a positive correlation between antibody avidity and protection. The antibodies in the protected mice recognized the native CSP on the parasites and showed sporozoite invasion inhibitory activity. Passive transfer of anti-CSP antibodies into naive mice also induced protection. Thus, we have demonstrated the utility of a mouse efficacy model to down-select human CSP-based vaccine formulations.
Development of a Singleplex PCR Assay for Rapid Identification and Differentiation of Cryptococcus neoformans var.grubii, Cryptococcus neoformans var. neoformans, Cryptococcus gattii, and Hybrids
Authors: Feng Xiaobo , Fu Xiaohua , Ling Bo , Wang Lei , Liao Wanqing , Yao Zhirong 
Published: March 2013

ABSTRACTA singleplex PCR assay using a single primer pair targeting the putative sugar transporter gene was developed here to distinguishCryptococcus neoformansvar.grubii,Cryptococcus neoformansvar.neoformans, andCryptococcus gattiiaccording to the distinct size of the amplicon. The interspecies and intravarietal hybrids were also characterized on the basis of distinct combined profiles of amplicons. This PCR assay is a rapid, simple, and reliable approach suitable for laboratory diagnoses and large-scale epidemiologic studies.
Does Neutralization of Gastric Aspirates from Children with Suspected Intrathoracic Tuberculosis Affect Mycobacterial Yields on MGIT Culture?
Authors: Parashar Deepak , Kabra Sushil K. , Lodha Rakesh , Singh Varinder , Mukherjee Aparna , Arya Tina , Grewal Harleen M. S. , Singh Sarman ,   Delhi Pediatric TB Study Group
Published: March 2013

ABSTRACT

The microbiological confirmation of pulmonary tuberculosis in children relies on cultures of gastric aspirate (GA) specimens. Conventionally, GAs are neutralized to improve culture yields of mycobacteria. However, there are limited data to support this practice. To study the utility of neutralization of GAs with sodium bicarbonate in children with intrathoracic tuberculosis, a total of 116 children of either sex, aged 6 months to 14 years (median age, 120 months; interquartile range [IQR], 7 to 192 months), underwent gastric aspiration on 2 consecutive days. Gastric aspirates were divided into two aliquots, and only one aliquot was neutralized with 1% sodium bicarbonate. Both aliquots were processed for smear and culture examinations. Out of the 232 gastric aspirates, 12 (5.17%) were acid-fast bacilli (AFB) smear positive. There were no differences in smear positivity rates from samples with or without neutralization. The yield of
Mycobacterium tuberculosis
on a Bactec MGIT 960 culture system was significantly lower in the neutralized samples (16.3% [38/232]) than in the nonneutralized samples (21.5% [50/232]) (
P
= 0.023). There was no significant difference between the neutralized and the nonneutralized samples in time to detection using the MGIT 960 system (average, 24.6 days; IQR, 12 to 37 days) (
P
= 0.9). The contamination rates were significantly higher in the neutralized samples than in the nonneutralized samples (17.2% [40/232] versus 3.9% [9/232]) (
P
= 0.001). The agreement for positive mycobacterial culture between the two approaches was 66.5% (
P
= 0.001). Hence, we recommend that gastric aspirate samples not be neutralized with sodium bicarbonate prior to culture for
M. tuberculosis
.
Detection of IMP Metallo-β-Lactamase in Carbapenem-Nonsusceptible Enterobacteriaceae and Non-Glucose-Fermenting Gram-Negative Rods by Immunochromatography Assay
Authors: Notake Shigeyuki , Matsuda Mari , Tamai Kiyoko , Yanagisawa Hideji , Hiramatsu Keiichi , Kikuchi Ken 
Published: March 2013

ABSTRACTMetallo-β-lactamases (MBLs) are transmissible carbapenemases of increasing prevalence in Gram-negative bacteria among health care facilities worldwide. Control of the further spread of these carbapenem-resistant bacteria relies on clinical microbiological laboratories correctly identifying and classifying the MBLs. In this study, we evaluated a simple and rapid method for detecting IMP, the most prevalent MBL in Japan. We used an immunochromatography (IC) assay for 181 carbapenem-nonsusceptible (CNS) (nonsusceptible to imipenem or meropenem) strains comprising 74 IMP-producing and 33 non-IMP-producing strains of non-glucose-fermenting Gram-negative rods (NFGNR), as well as 64 IMP-producing and 10 non-IMP-producingEnterobacteriaceaestrains. The IC assay results were compared to those from the double-disk synergy test (DDST), the MBL Etest, and the modified Hodge test (MHT) (only forEnterobacteriaceae). The IMP type was confirmed by specific PCR and direct sequencing. The IC assay detected all of the IMP-type MBLs, including IMP-1, -2, -6, -7, -10, -11, -19, -20, and -22 and IMP-40, -41, and -42 (new types), with 100% specificity and sensitivity against all strains tested. Although the sensitivity and specificity values for the DDST and MHT were equivalent to those for the IC assay, the MBL Etest was positive for only 87% of NFGNR and 31% ofEnterobacteriaceaedue to the low MIC of imipenem, causing an indeterminate evaluation. These results indicated that the IC assay might be a useful alternative to PCR for IMP MBL detection screening.
HIV-1 Gag Associates with Specific Uropod-Directed Microdomains in a Manner Dependent on Its MA Highly Basic Region
Authors: Llewellyn G. Nicholas , Grover Jonathan R. , Olety Balaji , Ono Akira 
Published: March 2013

ABSTRACT

In polarized T cells, HIV-1 Gag localizes to a rear-end protrusion known as the uropod in a multimerization-dependent manner. Gag-laden uropods participate in formation of virological synapses, intercellular contact structures that play a key role in cell-to-cell HIV-1 transmission. Our previous observations suggest that Gag associates with uropod-directed microdomains (UDMs) that eventually comigrate with Gag to the uropod over the cell surface. However, the nature of Gag multimerization required for this movement, the composition of the UDMs, and the molecular determinants for Gag association with these microdomains remain unknown. In this study, we found that Gag multimerization prior to budding but beyond dimerization is necessary for Gag localization to the uropods, indicating that uropod localization occurs early in the assembly process. We also found that prior to membrane curvature, Gag multimers associate with a specific subset of UDMs containing PSGL-1, CD43, and CD44 but not ICAM-1, ICAM-3, or CD59. Notably, upon association, Gag excludes ICAM-3 from this subset of UDMs, revealing an active and selective reorganization of these microdomains by Gag. This specific association between Gag and UDMs is dependent on the highly basic region (HBR) in the Gag matrix (MA) domain. The overall positive charge of the HBR was needed for the interaction with the specific UDM subset, while the exact HBR sequence was not, unlike that seen for MA binding to the plasma membrane phospholipid phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P
2
]. Taken totogether, these findings revealed that HIV-1 Gag associates with specific microdomains present in polarized T cells in an MA-dependent manner, which results in modification of the microdomain constituents.
Differential Recognition of Old World and New World Arenavirus Envelope Glycoproteins by Subtilisin Kexin Isozyme 1 (SKI-1)/Site 1 Protease (S1P)
Authors: Burri Dominique J. , Ramos da Palma Joel , Seidah Nabil G. , Zanotti Giuseppe , Cendron Laura , Pasquato Antonella , Kunz Stefan 
Published: March 2013

ABSTRACT
The arenaviruses are an important family of emerging viruses that includes several causative agents of severe hemorrhagic fevers in humans that represent serious public health problems. A crucial step of the arenavirus life cycle is maturation of the envelope glycoprotein precursor (GPC) by the cellular subtilisin kexin isozyme 1 (SKI-1)/site 1 protease (S1P). Comparison of the currently known sequences of arenavirus GPCs revealed the presence of a highly conserved aromatic residue at position P7 relative to the SKI-1/S1P cleavage side in Old World and clade C New World arenaviruses but not in New World viruses of clades A and B or cellular substrates of SKI-1/S1P. Using a combination of molecular modeling and structure-function analysis, we found that residueY285 of SKI-1/S1P, distal from the catalytic triad, is implicated in the molecular recognition of the aromatic “signature residue” at P7 in the GPC of Old World Lassa virus. Using a quantitative biochemical approach, we show that Y285 of SKI-1/S1P is crucial for the efficient processing of peptides derived from Old World and clade C New World arenavirus GPCs but not of those from clade A and B New World arenavirus GPCs. The data suggest that during coevolution with their mammalian hosts, GPCs of Old World and clade C New World viruses expanded the molecular contacts with SKI-1/S1P beyond the classical four-amino-acid recognition sequences and currently occupy an extended binding pocket.
Human Cytomegalovirus Induces a Biphasic Inflammatory Response in Primary Endothelial Cells
Authors: Jeffery H. C. , Söderberg-Naucler C. , Butler L. M. 
Published: March 2013

ABSTRACT

Contradictory studies report either pro- or anti-inflammatory endothelial cell (EC) responses to human cytomegalovirus (hCMV) infection, hindering the validation of a potential link between this virus and associated inflammatory pathologies. Clarifying this issue, we report that hCMV induces a biphasic response. Early after inoculation, hCMV promoted lymphocyte and, to a lesser extent, neutrophil capture under
in vivo
relevant shear stresses. In contrast, later stages of infection rendered EC refractory to basal, or cytokine-induced, leukocyte recruitment.
Role of E1B55K in E4orf6/E1B55K E3 Ligase Complexes Formed by Different Human Adenovirus Serotypes
Authors: Cheng Chi Ying , Gilson Timra , Wimmer Peter , Schreiner Sabrina , Ketner Gary , Dobner Thomas , Branton Philip E. , Blanchette Paola 
Published: March 2013

ABSTRACT
The E4orf6 protein of serotypes representing all human adenovirus species forms Cullin-based E3 ubiquitin ligase complexes that facilitate virus infection by inducing degradation of cellular proteins that impede efficient viral replication. This complex also includes the viral E1B55K product believed to bind and introduce substrates for ubiquitination. Heterogeneity in the composition of these ligases exists, as some serotypes form Cul5-based complexes whereas others utilize Cul2. Significant variations in substrate specificities also exist among serotypes, as some degrade certain substrates very efficiently whereas others induce more modest or little degradation. As E1B55K is believed to function as the substrate acquisition component of the ligase, we undertook studies to compare the ability of representative E1B55K proteins to bind substrates with the efficacy of degradation by their respective E4orf6-based ligases. Interestingly, although efficient degradation in some cases corresponded to the ability of E1B55K to bind to or relocalize substrates, there were several examples of substrates that bound efficiently to E1B55K but were not degraded and others in which substrates were degraded even though binding to E1B55K was low or undetectable. These results suggest that transient interactions with E1B55K may be sufficient for efficient substrate degradation and that binding alone is not sufficient, implying that the orientation of the substrate in the ligase complex is probably crucial. Nevertheless, we found that the substrate specificity of certain E4orf6-based ligases could be altered through the formation of hybrid complexes containing E1B55K from another serotype, thus confirming identification of E1B55K as the substrate acquisition component of the complex.