bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type-I interferon signaling through ISGF3 complex is required for sustained Rip3 activation and necroptosis in macrophages
Authors: McComb Scott , Cessford Erin , Alturki Norah A. , Joseph Julie , Shutinoski Bojan , Startek Justyna B. , Gamero Ana M. , Mossman Karen L. , Sad Subash 
Published: July 2014

SignificanceAlthough it has long been known that inflammatory immune responses are associated with death of cells through necrosis, the mechanisms controlling this process are not yet well understood. Recently a type of programmed inflammatory cell death, necroptosis, has been discovered. In this paper we reveal previously unidentified molecular mechanisms that operate to induce this form of cell death. Our results indicate that in order to undergo necroptosis, immune cells must produce and receive signals from the key immune regulator, interferon. Such interferon-dependent necroptosis of immune cells drives acute inflammatory pathology in a mouse model of sepsis. This work highlights the intimate connection between cell death and inflammation, and may lead to new understanding and treatment of inflammatory pathologies.
Auxin transport sites are visualized in planta using fluorescent auxin analogs
Authors: Hayashi Ken-ichiro , Nakamura Shouichi , Fukunaga Shiho , Nishimura Takeshi , Jenness Mark K. , Murphy Angus S. , Motose Hiroyasu , Nozaki Hiroshi , Furutani Masahiko , Aoyama Takashi 
Published: July 2014

Significance
Fluorescent auxin analogs are designed to function as active auxins for the auxin transport system but to be inactive for auxin signaling. These fluorescent auxin analogs can mimic auxin via the transport system and be used to visualize inter- and intracellular auxin distribution in roots. These analogs allow imaging of auxin transport sites with high spatiotemporal resolution. Our fluorescent auxin system provides insight into auxin transport dynamics and subcellular auxin distribution.
Critical role of canonical transient receptor potential channel 7 in initiation of seizures
Authors: Phelan Kevin D. , Shwe U Thaung , Abramowitz Joel , Birnbaumer Lutz , Zheng Fang 
Published: July 2014

Significance
Canonical transient receptor potential (TRPC) channels are a family of polymodal cation channels. TRPC7 was the last member of the TRPC family cloned, and the functional role of TRPC7 in the brain is completely unknown. Here, we show that genetic ablation of TRPC7 disrupts acute severe seizures induced by pilocarpine in mice. This disruption is associated with a reduction in pilocarpine-induced increase in gamma wave activity that precedes the acute seizures. At the cellular level, loss of TRPC7 shows reduced long-term potentiation at cornu ammonis (CA) 3 recurrent collateral synapses, which is critical for the generation of epileptiform burst firing in the CA3 region of the hippocampus. Our findings reveal a critical role for TRPC7 in the generation of seizures.
Blockade of oncogenic IκB kinase activity in diffuse large B-cell lymphoma by bromodomain and extraterminal domain protein inhibitors
Authors: Ceribelli Michele , Kelly Priscilla N. , Shaffer Arthur L. , Wright George W. , Xiao Wenming , Yang Yibin , Mathews Griner Lesley A. , Guha Rajarshi , Shinn Paul , Keller Jonathan M. , Liu Dongbo , Patel Paresma R. , Ferrer Marc , Joshi Shivangi , Nerle Sujata , Sandy Peter , Normant Emmanuel , Thomas Craig J. , Staudt Louis M. 
Published: July 2014

SignificanceThe activated B-cell–like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer that can only be cured in roughly 40% of cases. These malignant cells rely on the NF-κB signaling pathway for survival. Here, we report that genetic or pharmacologic interference with bromodomain and extraterminal domain (BET) chromatin proteins reduces NF-κB activity and ABC DLBCL viability. Unexpectedly, the mechanism involves inhibition of IκB kinase, the key cytoplasmic enzyme that activates the NF-κB pathway. The NF-κB pathway in ABC DLBCL is activated by B-cell receptor signaling, which can be blocked by the BTK kinase inhibitor ibrutinib. BET inhibitors synergized with ibrutinib to decrease growth of ABC DLBCL tumors in mouse models. BET inhibitors should be evaluated in ABC DLBCL clinical trials.
Characterization and immobilization on nickel-chelated Sepharose of a glutamate decarboxylase A from Lactobacillus brevis BH2 and its application for production of GABA
Authors: Lee Ji-Yeon , Jeon Sung-Jong 
Published: July 2014

Abstract
A gene encoding glutamate decarboxylase A (GadA) from Lactobacillus brevis BH2 was expressed in a His-tagged form in Escherichia coli cells, and recombinant protein exists as a homodimer consisting of identical subunits of 53 kDa. GadA was absolutely dependent on the ammonium sulfate concentration for catalytic activity and secondary structure formation. GadA was immobilized on the metal affinity resin with an immobilization yield of 95.8%. The pH optima of the immobilized enzyme were identical with those of the free enzyme. However, the optimum temperature for immobilized enzyme was 5 °C higher than that for the free enzyme. The immobilized GadA retained its relative activity of 41% after 30 reuses of reaction within 30 days and exhibited a half-life of 19 cycles within 19 days. A packed-bed bioreactor with immobilized GadA showed a maximum yield of 97.8% GABA from 50 mM l-glutamate in a flow-through system under conditions of pH 4.0 and 55 °C.
Enhanced levels of nicotianamine promote iron accumulation and tolerance to calcareous soil in soybean
Authors: Nozoye Tomoko , Kim Suyoen , Kakei Yusuke , Takahashi Michiko , Nakanishi Hiromi , Nishizawa Naoko K 
Published: July 2014

Abstract
Iron (Fe) is an essential nutrient in both plants and humans. Fe deficiency on calcareous soil with low Fe availability is a major agricultural problem. Nicotianamine (NA) is one of the Fe chelator in plants, which is involved in metal translocation into seeds, and serves as an antihypertensive substance in humans. In this study, soybean plants overexpressing the barley NA synthase 1 (HvNAS1) gene driven by the constitutive CaMV 35S promoter were produced using Agrobacterium-mediated transformation. The transgenic soybean showed no growth defect and grew normally. The NA content of transgenic soybean seeds was up to four-fold greater than that of non-transgenic (NT) soybean seeds. The level of HvNAS1 expression was positively correlated with the amount of NA, and a high concentration of NA was maintained in the seeds in succeeding generations. The Fe concentration was approximately two-fold greater in transgenic soybean seeds than in NT soybean seeds. Furthermore, the transgenic soybeans showed tolerance to low Fe availability in calcareous soil. Our results suggested that increasing the NA content in soybean seeds by the overexpression of HvNAS1 offers potential benefits for both human health and agricultural productivity.
De novo assembly, gene annotation, and simple sequence repeat marker development using Illumina paired-end transcriptome sequences in the pearl oyster Pinctada maxima
Authors: Deng Yuewen , Lei Qiannan , Tian Qunli , Xie Shaohe , Du Xiaodong , Li Junhui , Wang Liqun , Xiong Yuanxin 
Published: July 2014

Abstract
We analyzed the mantle transcriptome of pearl oyster Pinctada maxima and developed EST–SSR markers using Illumina HiSeq 2000 paired-end sequencing technology. A total of 49,500,748 raw reads were generated. De novo assembly generated 108,704 unigenes with an average length of 407 bp. Sequence similarity search with known proteins or nucleotides revealed that 30,200 (27.78%) and 25,824 (23.76%) consensus sequences were homologous with the sequences in the non-redundant protein and Swiss–Prot databases, respectively, and that 19,701 (18.12%) of these unigenes were possibly involved in approximately 234 known signaling pathways in the Kyoto Encyclopedia of Genes and Genomes database. Ninety one biomineralization-related unigenes were detected. In a cultured stock, 1764 simple sequence repeats were identified and 56 primer pairs were randomly selected and tested. The rate of successful amplification was 68.3%. The developed molecular markers are helpful for further studies on genetic linkage analysis, gene localization, and quantitative trait loci mapping.
First Report of Fusarium Wilt of Strawberry Caused by Fusarium oxysporum in Serbia
Authors: Stanković I. , Ristić D. , Vučurović A. , Milojević K. , Nikolić D. , Krstić B. , Bulajić A. 
Published: July 2014

Strawberry (Fragaria × ananassa Duch.) is the third most important berry crop in Serbia with average production ranging from 30,000 to 35,000 t on approximately 5,000 ha (2). In June 2013, symptoms of wilt and whole plant collapse were observed on approximately 25% plants growing in commercial strawberry crop of cv. Alba in the locality of Zablaće (Moravica district). Initial symptoms included leaf chlorosis and wilt, followed by withering and necrosis of older leaves and reduced fruit production, eventually leading to plant collapse and desiccations. Internal vascular tissues of the crown showed distinct brown reddish discoloration. Three small pieces of infected roots, petioles, or crown vascular tissues were surface disinfested with 2% NaOCl and placed on five potato dextrose agars (PDA) per sample. After 7 days incubation at 23°C under 12 h of fluorescent light, nine monoconidial isolates were obtained (1) forming colonies with light purple mycelia. Colonies produced numerous hyaline, oval to ellipsoid microconidia (5 to 15 × 2.5 to 4.5 μm, average 8.45 × 2.25 μm), 3 to 5 septate fusoid macroconidia with pedicellate bases (20 to 50 × 2.70 to 6 μm, average 32.35 × 3.25 μm from 100 measured) and chlamydospores. Morphological and growth features were similar to the descriptions of Fusarium oxysporum Schlechtend emend. Snyder & Hansen (1). Pathogenicity of one selected isolate (97-13) was tested by dipping for 15 min the roots of five plants of each cultivar: Alba, Arosa, Clery, and Roxana into a conidial suspension (1 × 106 conidia/ml) harvested from a 7-day-old culture on PDA. Control plants were dipped in sterile distilled water. The inoculated plants were transplanted into pots containing sterilized peat and maintained in the greenhouse at 25°C. Thirty to thirty-five days post-inoculation, all plants developed wilt symptoms and vascular discoloration of crown tissues from which F. oxysporum was successfully re-isolated using the same method as for isolation. No symptoms were observed on any of the control plants. Morphological identification was confirmed by amplification and sequencing of a portion of the translation elongation factor-1 alpha (EF-1α) gene. Total DNA was extracted directly from fungal mycelium with a DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) and PCR amplification performed with primers EF-1/EF-2 (4). Sequence analysis of EF-1α region revealed that Serbian isolate 97-13 (GenBank Accession No. KJ647280) shared 99 to 100% identity with the F. oxysporum sequences in GenBank. To our knowledge, this is the first report of Fusarium wilt on strawberry in Serbia. The presence of a new and potentially harmful disease may represent a serious constraint for strawberry production in Serbia. References: (1) J. F. Leslie and B. A. Summerell. The Fusarium Laboratory Manual, Blackwell Publishing, London, UK, 2006. (2) M. Nikolić et al. Acta Hort. 842:615, 2009. (3) K. O'Donnell et al. Proc. Natl. Acad. Sci. USA 95:2044, 1998.
First Report of the Root-Knot Nematode Meloidogyne enterolobii Infecting Jujube in China
Authors: Long H. B. , Bai C. , Peng J. , Zeng F. Y. 
Published: July 2014

Jujube (Ziziphus jujuba Mill.) is an economically-important fruit crop grown in Europe, Australia, and southern/eastern Asia. In China, it is often called red date and the fruit is used in traditional Chinese herbal medicine and wine. In February 2014, jujube plants growing in a sandy soil in Sanya, Hainan Province, China, were observed exhibiting symptoms of decline, including stunting, wilting, and no flowering or fruit set. Roots systems of sick plants (n = 20) had many galls, the typical symptoms of root-knot nematode infection, and the incidence of infection was 100%. These galls were formed in the primary, secondary, and tertiary roots. Meloidogyne spp. females and egg masses were dissected from the symptomatic roots. Each root contained about 72 females on average (n = 20). The perineal patterns of females (n = 10) were oval shaped with moderate to high dorsal arches and mostly lacking obvious lateral lines. Second-stage juveniles (n = 20) had large and triangular lateral lips and broad, bluntly rounded tail tips. These morphological characteristics are the same as those for Meloidogyne enterolobii Yang & Eisenback 1983 (5). Identification was further confirmed after DNA extraction from 12 nematodes. Part of the rDNA spanning the internal transcribed spacer (ITS) 1, 5.8S gene, and ITS2 was amplified with primers V5367/26S (TTGATTACGTCCCTGCCCTTT/TTTCACTCGCCGTTACTAAGG) (4). A 764-bp fragment was amplified, which was 100% identical to sequences of M. enterolobii (GenBank Accession Nos. KJ146863, KF418369, JQ082448, and JX024149) in GenBank. Species identification was confirmed by using PCR to amplify mitochondrial (mt) DNA and rDNA intergenic spacers (IGS) 2 with primers C2F3/1108 (GGTCAATGTTCAGAAATTTGTGG/TACCTTTGACCAATCACGCT) (3) and M. enterolobii specific primers Me-F/Me-R (AACTTTTGTGAAAGTGCCGCTG/TCAGTTCAGGCAGGATCAACC), respectively (2). The PCR products were approximately 700 bp for mtDNA and 200 bp for rDNA-IGS2, which were also identical to those previously reported for M. enterolobii (2,3). M. enterolobii is considered as one of the most damaging root-knot nematode species due to its wide host range, high reproduction rate, and ability to overcome the resistance genes (Mi-1, Mh, Mir1, N, Tabasco, and Rk) in several crops (1). It is reported that over 20 plant species from eight families (Annonaceae, Apiaceae, Cucurbitaceae, Convolvulaceae, Fabaceae, Marantaceae, Myrtaceae, and Solanaceae) in China are hosts for M. enterolobii. To our knowledge, this is the first report of jujube as a host of M. enterolobii and the first record of M. enterolobii as a parasite of a plant in the family Rhamnaceae in China. References: (1) P. Castagnone-Sereno. Nematology 14:133, 2002. (2) H. Long et al. Acta Phytopathol. Sinica 36:109, 2006. (3) T. O. Powers and T. S. Harris. J. Nematol. 25:1, 1993. (4) T. C. Vrain et al. Fundam. Appl. Nematol. 15:565, 1992. (5) B. Yang and J. D. Eisenback. J. Nematol. 15:381, 1983.
Clinical Assessment of Auto-positive End-expiratory Pressure by Diaphragmatic Electrical Activity during Pressure Support and Neurally Adjusted Ventilatory Assist
Authors: Bellani Giacomo , Coppadoro Andrea , Patroniti Nicolò , Turella Marta , Arrigoni Marocco Stefano , Grasselli Giacomo , Mauri Tommaso , Pesenti Antonio 
Published: July 2014

Abstract

Background:
Auto-positive end-expiratory pressure (auto-PEEP) may substantially increase the inspiratory effort during assisted mechanical ventilation. Purpose of this study was to assess whether the electrical activity of the diaphragm (EAdi) signal can be reliably used to estimate auto-PEEP in patients undergoing pressure support ventilation and neurally adjusted ventilatory assist (NAVA) and whether NAVA was beneficial in comparison with pressure support ventilation in patients affected by auto-PEEP.

Methods:
In 10 patients with a clinical suspicion of auto-PEEP, the authors simultaneously recorded EAdi, airway, esophageal pressure, and flow during pressure support and NAVA, whereas external PEEP was increased from 2 to 14 cm H2O. Tracings were analyzed to measure apparent “dynamic” auto-PEEP (decrease in esophageal pressure to generate inspiratory flow), auto-EAdi (EAdi value at the onset of inspiratory flow), and IDEAdi (inspiratory delay between the onset of EAdi and the inspiratory flow).

Results:
The pressure necessary to overcome auto-PEEP, auto-EAdi, and IDEAdi was significantly lower in NAVA as compared with pressure support ventilation, decreased with increase in external PEEP, although the effect of external PEEP was less pronounced in NAVA. Both auto-EAdi and IDEAdi were tightly correlated with auto-PEEP (r
2 = 0.94 and r
2 = 0.75, respectively). In the presence of auto-PEEP at lower external PEEP levels, NAVA was characterized by a characteristic shape of the airway pressure.

Conclusions:
In patients with auto-PEEP, NAVA, compared with pressure support ventilation, led to a decrease in the pressure necessary to overcome auto-PEEP, which could be reliably monitored by the electrical activity of the diaphragm before inspiratory flow onset (auto-EAdi).
Effect of Hydroxyethyl Starch on Postoperative Kidney Function in Patients Having Noncardiac Surgery
Authors: Kashy Babak Kateby , Podolyak Attila , Makarova Natalya , Dalton Jarrod E. , Sessler Daniel I. , Kurz Andrea 
Published: July 2014

Abstract

Background:
Whether intraoperative use of hydroxyethyl starch impairs kidney function remains unknown. The authors thus tested the primary hypothesis that Hextend promotes renal injury in surgical patients. Secondarily, the authors evaluated the dose–outcome relationship, in-hospital and 90-day mortality, and whether the relationship between colloid use and acute kidney injury (AKI) depends on baseline risk for AKI.

Methods:
The authors evaluated the data of 44,176 adults without preexisting kidney failure who had inpatient noncardiac surgery from 2005 to 2012. Patients given a combination of colloid and crystalloid were propensity matched on morphometric, and baseline characteristics to patients given only crystalloid. The primary analysis was a proportional odds logistic regression with AKI as an ordinal outcome based on the Acute Kidney Injury Network classification.

Results:
The authors matched 14,680 patients receiving colloids with 14,680 patients receiving noncolloids for a total of 29,360 patients. After controlling for potential confounding variables, the odds of developing a more serious level of AKI with Hextend was 21% (6 to 38%) greater than with crystalloid only (P = 0.001). AKI risk increased as a function of colloid volume (P < 0.001). In contrast, the relationship between colloid use and AKI did not differ on baseline AKI risk (P = 0.84). There was no association between colloid use and risk of in-hospital (P = 0.81) or 90-day (P = 0.02) mortality.

Conclusion:
Dose-dependent renal toxicity associated with Hextend in patients having noncardiac surgery is consistent with randomized trials in critical care patients.
Selection of chromosomal DNA libraries using a multiplex CRISPR system inSaccharomyces cerevisiae
Authors: Ryan Owen W. , Skerker Jeffrey M. , Maurer Matthew J. , Li Xin , Tsai Jordan C. , Poddar Snigdha , Lee Michael E. , DeLoache Will , Dueber John E. , Arkin Adam P. , Cate Jamie H. D. 
Published: July 2014

AbstractThe directed evolution of biomolecules to improve or change their activity is central to many engineering and synthetic biology efforts. However, selecting improved variants from gene libraries in living cells requires plasmid expression systems that suffer from variable copy number effects, or the use of complex marker-dependent chromosomal integration strategies. We developed quantitative gene assembly and DNA library insertion into theSaccharomyces cerevisiaegenome by optimizing an efficient single-step and marker-free genome editing system using CRISPR-Cas9. With this Multiplex CRISPR (CRISPRm) system, we selected an improved cellobiose utilization pathway in diploid yeast in a single round of mutagenesis and selection, which increased cellobiose fermentation rates by over ten-fold. Mutations recovered in the best cellodextrin transporters reveal synergy between substrate binding and transporter dynamics, and demonstrate the power of CRISPRm to accelerate selection experiments and discoveries of the molecular determinants that enhance biomolecule function.
Efficient site-specific editing of theC. elegansgenome
Authors: Zhang Donglei , Glotzer Michael 
Published: July 2014

ABSTRACTIn just two years, genome editing with the CRISPR-associated endonuclease Cas9 has transformed genetic analysis in conventional and emerging model organisms. The efficiency of this method varies among systems and continues to be optimized. Numerous strategies have been reported for editing theC. elegansgenome. To date, these strategies do not provide a simple, rapid and inexpensive means to introduce and isolate arbitrary point mutants. Here, we report a strategy with all three of these desirable properties. It utilizes oligonucleotides as donor templates for homology-dependent repair and visible markers that are edited in parallel that markedly reduce the number of animals that must be molecularly screened in order to isolate mutants that lack visible phenotypes.
ASCORBATE PEROXIDASE6 Protects Arabidopsis Desiccating and Germinating Seeds from Stress and Mediates Cross Talk between Reactive Oxygen Species, Abscisic Acid, and Auxin
Authors: Chen Changming , Letnik Ilya , Hacham Yael , Dobrev Petre , Ben-Daniel Bat-Hen , Vanková Radomíra , Amir Rachel , Miller Gad 
Published: July 2014

AbstractA seed’s ability to properly germinate largely depends on its oxidative poise. The level of reactive oxygen species (ROS) in Arabidopsis (Arabidopsis thaliana) is controlled by a large gene network, which includes the gene coding for the hydrogen peroxide-scavenging enzyme, cytosolic ASCORBATE PEROXIDASE6 (APX6), yet its specific function has remained unknown. In this study, we show that seeds lacking APX6 accumulate higher levels of ROS, exhibit increased oxidative damage, and display reduced germination on soil under control conditions and that these effects are further exacerbated under osmotic, salt, or heat stress. In addition, ripening APX6-deficient seeds exposed to heat stress displayed reduced germination vigor. This, together with the increased abundance of APX6 during late stages of maturation, indicates that APX6 activity is critical for the maturation-drying phase. Metabolic profiling revealed an altered activity of the tricarboxylic acid cycle, changes in amino acid levels, and elevated metabolism of abscisic acid (ABA) and auxin in drying apx6 mutant seeds. Further germination assays showed an impaired response of the apx6 mutants to ABA and to indole-3-acetic acid. Relative suppression of abscisic acid insensitive3 (ABI3) and ABI5 expression, two of the major ABA signaling downstream components controlling dormancy, suggested that an alternative signaling route inhibiting germination was activated. Thus, our study uncovered a new role for APX6, in protecting mature desiccating and germinating seeds from excessive oxidative damage, and suggested that APX6 modulate the ROS signal cross talk with hormone signals to properly execute the germination program in Arabidopsis.