bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sea level regulated tetrapod diversity dynamics through the Jurassic/Cretaceous interval
Authors: Tennant Jonathan P. , Mannion Philip D. , Upchurch Paul 
Published: September 2016

AbstractReconstructing deep time trends in biodiversity remains a central goal for palaeobiologists, but our understanding of the magnitude and tempo of extinctions and radiations is confounded by uneven sampling of the fossil record. In particular, the Jurassic/Cretaceous (J/K) boundary, 145 million years ago, remains poorly understood, despite an apparent minor extinction and the radiation of numerous important clades. Here we apply a rigorous subsampling approach to a comprehensive tetrapod fossil occurrence data set to assess the group’s macroevolutionary dynamics through the J/K transition. Although much of the signal is exclusively European, almost every higher tetrapod group was affected by a substantial decline across the boundary, culminating in the extinction of several important clades and the ecological release and radiation of numerous modern tetrapod groups. Variation in eustatic sea level was the primary driver of these patterns, controlling biodiversity through availability of shallow marine environments and via allopatric speciation on land.
Osteoblasts secrete miRNA-containing extracellular vesicles that enhance expansion of human umbilical cord blood cells
Authors: Morhayim Jess , van de Peppel Jeroen , Braakman Eric , Rombouts Elwin W. J. C. , ter Borg Mariette N. D. , Dudakovic Amel , Chiba Hideki , van der Eerden Bram C. J. , Raaijmakers Marc H. , van Wijnen Andre J. , Cornelissen Jan J. , van Leeuwen Johannes P. 
Published: September 2016

AbstractOsteolineage cells represent one of the critical bone marrow niche components that support maintenance of hematopoietic stem and progenitor cells (HSPCs). Recent studies demonstrate that extracellular vesicles (EVs) regulate stem cell development via horizontal transfer of bioactive cargo, including microRNAs (miRNAs). Using next-generation sequencing we show that human osteoblast-derived EVs contain highly abundant miRNAs specifically enriched in EVs, including critical regulators of hematopoietic proliferation (e.g., miR-29a). EV treatment of human umbilical cord blood-derived CD34+ HSPCs alters the expression of candidate miRNA targets, such as HBP1, BCL2 and PTEN. Furthermore, EVs enhance proliferation of CD34+ cells and their immature subsets in growth factor-driven ex vivo expansion cultures. Importantly, EV-expanded cells retain their differentiation capacity in vitro and successfully engraft in vivo. These discoveries reveal a novel osteoblast-derived EV-mediated mechanism for regulation of HSPC proliferation and warrant consideration of EV-miRNAs for the development of expansion strategies to treat hematological disorders.
A Nucleus-Encoded Chloroplast Protein YL1 Is Involved in Chloroplast Development and Efficient Biogenesis of Chloroplast ATP Synthase in Rice
Authors: Chen Fei , Dong Guojun , Wu Limin , Wang Fang , Yang Xingzheng , Ma Xiaohui , Wang Haili , Wu Jiahuan , Zhang Yanli , Wang Huizhong , Qian Qian , Yu Yanchun 
Published: September 2016

AbstractChloroplast ATP synthase (cpATPase) is an importance thylakoid membrane-associated photosynthetic complex involved in the light-dependent reactions of photosynthesis. In this study, we isolated and characterized a rice (Oryza sativa) mutant yellow leaf 1 (yl1), which exhibits chlorotic leaves throughout developmental stages. The YL1 mutation showed reduced chlorophyll contents, abnormal chloroplast morphology and decreased photochemical efficiency. Moreover, YL1 deficiency disrupts the expression of genes associated with chloroplast development and photosynthesis. Molecular and genetic analyses revealed that YL1 is a nucleus-encoded protein with a predicted transmembrane domain in its carboxyl-terminus that is conserved in the higher plant kingdom. YL1 localizes to chloroplasts and is preferentially expressed in green tissues containing chloroplasts. Immunoblot analyses showed that inactivation of YL1 leads to drastically reduced accumulation of AtpA (α) and AtpB (β), two core subunits of CF1αβ subcomplex of cpATPase, meanwhile, a severe decrease (ca. 41.7%) in cpATPase activity was observed in the yl1-1 mutant compared with the wild type. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation assays revealed a specific interaction between YL1 and AtpB subunit of cpATPase. Taken together, our results suggest that YL1 is a plant lineage-specific auxiliary factor involved in the biogenesis of the cpATPase complex, possibly via interacting with the β-subunit.
The Efficacy of Lidocaine in Laryngospasm Prevention in Pediatric Surgery: a Network Meta-analysis
Authors: Qi Xiaojing , Lai Zhoupeng , Li Si , Liu Xiaochen , Wang Zhongxing , Tan Wulin 
Published: September 2016

AbstractHigher incidence and worse outcomes of laryngospasm during general anesthesia in children than adults have been reported for many years, but few prevention measures are put forward. Efficacy of lidocaine in laryngospasm prevention has been argued for many years and we decided to design this network meta-analysis to assess the efficacy of lidocaine. We conducted an electronic search of six sources and finally included 12 Randomized Controlled Trials including 1416 patients. A direct comparison between lidocaine and placebo revealed lidocaine had the effect on preventing laryngospasm in pediatric surgery (RR = 0.46, 95% CI = [0.30, 0.70], P = 0.0002, I2 = 0%). Both subgroup analysis and network analysis demonstrated that both intravenous lidocaine (subgroup: RR = 0.39, 95% CI = [0.18, 0.86], P = 0.02, I2 = 38%; network: RR = 0.25, 95% CI = [0.04, 0.86]) and topical lidocaine (subgroup: RR = 0.37, 95% CI = [0.19, 0.72], P = 0.003, I2 = 0%; network: RR = 0.14, 95% CI = [0.02, 0.55]) was effective in laryngospasm prevention, while no statistical difference was found in a comparison between intravenous and topical lidocaine. In conclusion, both intravenous and topical lidocaine are effective in laryngospasm prevention in pediatric surgery, while a comparison between them needs more evidences.
Identification of mutations through dominant screening for obesity using C57BL/6 substrains
Authors: Hossain Mohammad Sarowar , Asano Fuyuki , Fujiyama Tomoyuki , Miyoshi Chika , Sato Makito , Ikkyu Aya , Kanno Satomi , Hotta Noriko , Kakizaki Miyo , Honda Takato , Kim Staci J. , Komiya Haruna , Miura Ikuo , Suzuki Tomohiro , Kobayashi Kimio , Kaneda Hideki , Kumar Vivek , Takahashi Joseph S. , Wakana Shigeharu , Funato Hiromasa , Yanagisawa Masashi 
Published: September 2016

AbstractThe discovery of leptin substantiated the usefulness of a forward genetic approach in elucidating the molecular network regulating energy metabolism. However, no successful dominant screening for obesity has been reported, which may be due to the influence of quantitative trait loci between the screening and counter strains and the low fertility of obese mice. Here, we performed a dominant screening for obesity using C57BL/6 substrains, C57BL/6J and C57BL/6N, with the routine use of in vitro fertilization. The screening of more than 5000 mutagenized mice established two obese pedigrees in which single nucleotide substitutions in Mc4r and Sim1 genes were identified through whole-exome sequencing. The mutation in the Mc4r gene produces a premature stop codon and the mutant SIM1 protein lacks transcriptional activity, showing that the haploinsufficiency of SIM1 and MC4R results in obesity. We further examined the hypothalamic neuropeptide expressions in the mutant pedigrees and mice with diet-induced obesity, which showed that each obesity mouse model has distinct neuropeptide expression profiles. This forward genetic screening scheme is useful and applicable to any research field in which mouse models work.
Replication Timing of Human Telomeres is Conserved during Immortalization and Influenced by Respective Subtelomeres
Authors: Piqueret-Stephan Laure , Ricoul Michelle , Hempel William M. , Sabatier Laure 
Published: September 2016

AbstractTelomeres are specific structures that protect chromosome ends and act as a biological clock, preventing normal cells from replicating indefinitely. Mammalian telomeres are replicated throughout S-phase in a predetermined order. However, the mechanism of this regulation is still unknown. We wished to investigate this phenomenon under physiological conditions in a changing environment, such as the immortalization process to better understand the mechanism for its control. We thus examined the timing of human telomere replication in normal and SV40 immortalized cells, which are cytogenetically very similar to cancer cells. We found that the timing of telomere replication was globally conserved under different conditions during the immortalization process. The timing of telomere replication was conserved despite changes in telomere length due to endogenous telomerase reactivation, in duplicated homologous chromosomes and in rearranged chromosomes. Importantly, translocated telomeres, possessing their initial subtelomere, retained the replication timing of their homolog, independently of the proportion of the translocated arm, even when the remaining flanking DNA is restricted to its subtelomere, the closest chromosome-specific sequences (inferior to 500 kb). Our observations support the notion that subtelomere regions strongly influence the replication timing of the associated telomere.
Projected loss of soil organic carbon in temperate agricultural soils in the 21st century: effects of climate change and carbon input trends
Authors: Wiesmeier Martin , Poeplau Christopher , Sierra Carlos A. , Maier Harald , Frühauf Cathleen , Hübner Rico , Kühnel Anna , Spörlein Peter , Geuß Uwe , Hangen Edzard , Schilling Bernd , von Lützow Margit , Kögel-Knabner Ingrid 
Published: September 2016

AbstractClimate change and stagnating crop yields may cause a decline of SOC stocks in agricultural soils leading to considerable CO2 emissions and reduced agricultural productivity. Regional model-based SOC projections are needed to evaluate these potential risks. In this study, we simulated the future SOC development in cropland and grassland soils of Bavaria in the 21st century. Soils from 51 study sites representing the most important soil classes of Central Europe were fractionated and derived SOC pools were used to initialize the RothC soil carbon model. For each site, long-term C inputs were determined using the C allocation method. Model runs were performed for three different C input scenarios as a realistic range of projected yield development. Our modelling approach revealed substantial SOC decreases of 11–16% under an expected mean temperature increase of 3.3 °C assuming unchanged C inputs. For the scenario of 20% reduced C inputs, agricultural SOC stocks are projected to decline by 19–24%. Remarkably, even the optimistic scenario of 20% increased C inputs led to SOC decreases of 3–8%. Projected SOC changes largely differed among investigated soil classes. Our results indicated that C inputs have to increase by 29% to maintain present SOC stocks in agricultural soils.
Astragaloside IV ameliorates renal injury in db/db mice
Authors: Sun Huili , Wang Wenjing , Han Pengxun , Shao Mumin , Song Gaofeng , Du Heng , Yi Tiegang , Li Shunmin 
Published: September 2016

AbstractDiabetic nephropathy is a lethal complication of diabetes mellitus and a major type of chronic kidney disease. Dysregulation of the Akt pathway and its downstream cascades, including mTOR, NFκB, and Erk1/2, play a critical role in the development of diabetic nephropathy. Astragaloside IV is a major component of Huangqi and exerts renal protection in a mouse model of type 1 diabetes. The current study was undertaken to investigate the protective effects of diet supplementation of AS-IV on renal injury in db/db mice, a type 2 diabetic mouse model. Results showed that administration of AS-IV reduced albuminuria, ameliorated changes in the glomerular and tubular pathology, and decreased urinary NAG, NGAL, and TGF-β1 in db/db mice. AS-IV also attenuated the diabetes-related activation of Akt/mTOR, NFκB, and Erk1/2 signaling pathways without causing any detectable hepatotoxicity. Collectively, these findings showed AS-IV to be beneficial to type 2 diabetic nephropathy, which might be associated with the inhibition of Akt/mTOR, NFκB and Erk1/2 signaling pathways.
Association between Oxidative DNA Damage and Risk of Colorectal Cancer: Sensitive Determination of Urinary 8-Hydroxy-2′-deoxyguanosine by UPLC-MS/MS Analysis
Authors: Guo Cheng , Li Xiaofen , Wang Rong , Yu Jiekai , Ye Minfeng , Mao Lingna , Zhang Suzhan , Zheng Shu 
Published: September 2016

AbstractOxidative DNA damage plays crucial roles in the pathogenesis of numerous diseases including cancer. 8-hydroxy-2′-deoxyguanosine (8-OHdG) is the most representative product of oxidative modifications of DNA, and urinary 8-OHdG is potentially the best non-invasive biomarker of oxidative damage to DNA. Herein, we developed a sensitive, specific and accurate method for quantification of 8-OHdG in human urine. The urine samples were pretreated using off-line solid-phase extraction (SPE), followed by ultrahigh performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis. By the use of acetic acid as an additive to the mobile phase, we improved the UPLC-MS/MS detection of 8-OHdG by 2.7−5.3 times. Using the developed strategy, we measured the contents of 8-OHdG in urine samples from 142 healthy volunteers and 84 patients with colorectal cancer (CRC). We observed increased levels of urinary 8-OHdG in patients with CRC and patients with tumor metastasis, compared to healthy controls and patients without tumor metastasis, respectively. Additionally, logistic regression analysis and receiver operator characteristic (ROC) curve analysis were performed. Our findings implicate that oxidative stress plays important roles in the development of CRC and the marked increase of urinary 8-OHdG may serve as a potential liquid biomarker for the risk estimation, early warning and detection of CRC.
Comprehensive analysis of SET domain gene family in foxtail millet identifies the putative role of SiSET14 in abiotic stress tolerance
Authors: Yadav Chandra Bhan , Muthamilarasan Mehanathan , Dangi Anand , Shweta Shweta , Prasad Manoj 
Published: September 2016

AbstractSET domain-containing genes catalyse histone lysine methylation, which alters chromatin structure and regulates the transcription of genes that are involved in various developmental and physiological processes. The present study identified 53 SET domain-containing genes in C4 panicoid model, foxtail millet (Setaria italica) and the genes were physically mapped onto nine chromosomes. Phylogenetic and structural analyses classified SiSET proteins into five classes (I–V). RNA-seq derived expression profiling showed that SiSET genes were differentially expressed in four tissues namely, leaf, root, stem and spica. Expression analyses using qRT-PCR was performed for 21 SiSET genes under different abiotic stress and hormonal treatments, which showed differential expression of these genes during late phase of stress and hormonal treatments. Significant upregulation of SiSET gene was observed during cold stress, which has been confirmed by over-expressing a candidate gene, SiSET14 in yeast. Interestingly, hypermethylation was observed in gene body of highly differentially expressed genes, whereas methylation event was completely absent in their transcription start sites. This suggested the occurrence of demethylation events during various abiotic stresses, which enhance the gene expression. Altogether, the present study would serve as a base for further functional characterization of SiSET genes towards understanding their molecular roles in conferring stress tolerance.
High-Throughput Screening of Coenzyme Preference Change of Thermophilic 6-Phosphogluconate Dehydrogenase from NADP+ to NAD+
Authors: Huang Rui , Chen Hui , Zhong Chao , Kim Jae Eung , Zhang Yi-Heng Percival 
Published: September 2016

AbstractCoenzyme engineering that changes NAD(P) selectivity of redox enzymes is an important tool in metabolic engineering, synthetic biology, and biocatalysis. Here we developed a high throughput screening method to identify mutants of 6-phosphogluconate dehydrogenase (6PGDH) from a thermophilic bacterium Moorella thermoacetica with reversed coenzyme selectivity from NADP+ to NAD+. Colonies of a 6PGDH mutant library growing on the agar plates were treated by heat to minimize the background noise, that is, the deactivation of intracellular dehydrogenases, degradation of inherent NAD(P)H, and disruption of cell membrane. The melted agarose solution containing a redox dye tetranitroblue tetrazolium (TNBT), phenazine methosulfate (PMS), NAD+, and 6-phosphogluconate was carefully poured on colonies, forming a second semi-solid layer. More active 6PGDH mutants were examined via an enzyme-linked TNBT-PMS colorimetric assay. Positive mutants were recovered by direct extraction of plasmid from dead cell colonies followed by plasmid transformation into E. coli TOP10. By utilizing this double-layer screening method, six positive mutants were obtained from two-round saturation mutagenesis. The best mutant 6PGDH A30D/R31I/T32I exhibited a 4,278-fold reversal of coenzyme selectivity from NADP+ to NAD+. This screening method could be widely used to detect numerous redox enzymes, particularly for thermophilic ones, which can generate NAD(P)H reacted with the redox dye TNBT.
High minimum inhibitory concentration of imipenem as a predictor of fatal outcome in patients with carbapenem non-susceptible Klebsiella pneumoniae
Authors: Wu Ping-Feng , Chuang Chien , Su Chin-Fang , Lin Yi-Tsung , Chan Yu-Jiun , Wang Fu-Der , Chuang Yin-Ching , Siu L. Kristopher , Fung Chang-Phone 
Published: September 2016

AbstractCarbapenem resistance in Klebsiella pneumoniae is important because of its increasing prevalence and limited therapeutic options. To investigate the clinical and microbiological characteristics of patients infected or colonized with carbapenem non-susceptible K. pneumoniae (CnsKP) in Taiwan, we conducted a retrospective study at Taipei Veterans General Hospital from January 2012 to November 2013. Carbapenem non-susceptibility was defined as a minimum inhibitory concentration (MIC) of ≥2 mg/L for imipenem or meropenem. A total of 105 cases with CnsKP were identified: 49 patients with infection and 56 patients with colonization. Thirty-one isolates had genes that encoded carbapenemases (29.5%), including K. pneumoniae carbapenemase (KPC)-2 (n = 27), KPC-3 (n = 1), VIM-1 (n = 1) and IMP-8 (n = 2). The in-hospital mortality among patients with CnsKP was 43.8%. A MIC for imipenem ≥16 μg/mL, nasogastric intubation and Acute Physiology and Chronic Health Evaluation II score were independent risk factors for in-hospital mortality for all patients with CnsKP. A MIC for imipenem ≥16 μg/mL was also an independent risk factor for 14-day mortality in patients with CnsKP. In conclusion, a positive culture for CnsKP was associated with high in-hospital mortality. A high imipenem MIC of CnsKP can predispose a patient to a poor prognosis.
Non-Host Plant Volatiles Disrupt Sex Pheromone Communication in a Specialist Herbivore
Authors: Wang Fumin , Deng Jianyu , Schal Coby , Lou Yonggen , Zhou Guoxin , Ye Bingbing , Yin Xiaohui , Xu Zhihong , Shen Lize 
Published: September 2016

AbstractThe ecological effects of plant volatiles on herbivores are manifold. Little is known, however, about the impacts of non-host plant volatiles on intersexual pheromonal communication in specialist herbivores. We tested the effects of several prominent constitutive terpenoids released by conifers and Eucalyptus trees on electrophysiological and behavioral responses of an oligophagous species, Plutella xylostella, which feeds on Brassicaceae. The non-host plant volatile terpenoids adversely affected the calling behavior (pheromone emission) of adult females, and the orientation responses of adult males to sex pheromone were also significantly inhibited by these terpenoids in a wind tunnel and in the field. We suggest that disruption of both pheromone emission and orientation to sex pheromone may explain, at least in part, an observed reduction in herbivore attack in polyculture compared with monoculture plantings. We also propose that mating disruption of both male and female moths with non-host plant volatiles may be a promising alternative pest management strategy.
SIRT2 activates G6PD to enhance NADPH production and promote leukaemia cell proliferation
Authors: Xu Shuang-Nian , Wang Tian-Shi , Li Xi , Wang Yi-Ping 
Published: September 2016

AbstractLike most other types of cancer cells, leukaemia cells undergo metabolic reprogramming to support rapid proliferation through enhancing biosynthetic processes. Pentose phosphate pathway (PPP) plays a pivotal role in meeting the anabolic demands for cancer cells. However, the molecular mechanism by which PPP contributes to leukaemia remains elusive. Here, we report that leukaemia cell proliferation is dependent on the oxidative branch of PPP, in particular the first and rate-limiting enzyme glucose-6-phosphate dehydrogenase (G6PD). Knockdown of G6PD reduces NADPH level in acute myeloid leukaemia (AML) cell lines. Exogenous lipid supplements partially restore the proliferation of G6PD-depleted cells. Deacetylase SIRT2 promotes NADPH production through deacetylating G6PD at lysine 403 (K403). Activation of G6PD by SIRT2 supports the proliferation and clonogenic activity of leukaemia cells. Chemical inhibitors against SIRT2 suppress G6PD activity, leading to reduced cell proliferation of leukaemia cells, but not normal hematopoietic stem and progenitor cells. Importantly, SIRT2 is overexpressed in clinical AML samples, while K403 acetylation is downregulated and G6PD catalytic activity is increased comparing to that of normal control. Together, our study reveals that acetylation regulation of G6PD is involved in the metabolic reprogramming of AML, and SIRT2 serves as a promising target for further therapeutic investigations.
Changes in SBPase activity influence photosynthetic capacity, growth, and tolerance to chilling stress in transgenic tomato plants
Authors: Ding Fei , Wang Meiling , Zhang Shuoxin , Ai Xizhen 
Published: September 2016

AbstractSedoheptulose-1, 7-bisphosphatase (SBPase) is an important enzyme involved in photosynthetic carbon fixation in the Calvin cycle. Here, we report the impact of changes in SBPase activity on photosynthesis, growth and development, and chilling tolerance in SBPase antisense and sense transgenic tomato (Solanum lycopersicum) plants. In transgenic plants with increased SBPase activity, photosynthetic rates were increased and in parallel an increase in sucrose and starch accumulation was evident. Total biomass and leaf area were increased in SBPase sense plants, while they were reduced in SBPase antisense plants compared with equivalent wild-type tomato plants. Under chilling stress, when compared with plants with decreased SBPase activity, tomato plants with increased SBPase activity were found to be more chilling tolerant as indicated by reduced electrolyte leakage, increased photosynthetic capacity, and elevated RuBP regeneration rate and quantum efficiency of photosystem II. Collectively, our data suggest that higher level of SBPase activity gives an advantage to photosynthesis, growth and chilling tolerance in tomato plants. This work also provides a case study that an individual enzyme in the Calvin cycle may serve as a useful target for genetic engineering to improve production and stress tolerance in crops.