bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensis Sonn.) fruits during early development
Authors: Liu Wei , Chen Maoshan , Bai Lijun , Zhuang Zhenhua , Fan Chao , Jiang Nonghui , Zhao Junsheng , Ma Shuaipeng , Xiang Xu 
Published: July 2017

AbstractLitchi (Litchi chinensis Sonn.) is an important fruit that is widely cultivated in tropical and subtropical areas. In this study, we used RNA-Seq and iTRAQ technologies to compare the transcriptomes and proteomes of pollinated (polLFs) and parthenocarpic (parLFs) litchi fruits during early development (1 day, 2 days, 4 days and 6 days). We identified 4,864 DEGs in polLFs and 3,672 in parLFs, of which 2,835 were shared and 1,051 were specifically identified in parLFs. Compared to po1LFs, 768 DEGs were identified in parLFs. iTRAQ analysis identified 551 DEPs in polLFs and 1,021 in parLFs, of which 305 were shared and 526 were exclusively identified in parLFs. We found 1,127 DEPs in parLFs compared to polLFs at different stages. Further analysis revealed some DEGs/DEPs associated with abscisic acid, auxin, ethylene, gibberellin, heat shock protein (HSP), histone, ribosomal protein, transcription factor and zinc finger protein (ZFP). WGCNA identified a large set of co-expressed genes/proteins in polLFs and parLFs. In addition, a cross-comparison of transcriptomic and proteomic data identified 357 consistent DEGs/DEPs in polLFs and parLFs. This is the first time that protein/gene changes have been studied in polLFs and parLFs, and the findings improve our understanding of litchi parthenocarpy.
Self-diffusivity, M–S and Fick diffusivity of CO2 in Na-clay: The influences of concentration and temperature
Authors: Hu Haixiang , Xing Yanfei , Li Xiaochun 
Published: July 2017

AbstractStoring CO2 in underground saline aquifers is an important way to reduce CO2 emission in atmosphere, where gas/fluid diffusion in clay plays a key role in CO2 leakage and migration. Various diffusivities, self-diffusivity, Maxwell–Stefan (M–S) diffusivity and Fick diffusivity, in clay interlayer are investigated by molecular dynamics (MD). Self-diffusivity varies with CO2 concentration, and reaches the maximum value at 2 molecules/unit-cell. High fluid concentration leads to clay swelling, thereby increasing self-diffusivity. However, the fractional free volume of clay explains the trend of CO2 self-diffusivity, which does not decrease with CO2 concentration monotonously but reaches the maximum when CO2 concentration reaches 2. Displacement distribution of CO2 molecules is analysed to explore the microscopic diffusion mechanism, which is characterised by logarithmic normal distribution. The mean value of such distribution further explains the self-diffusivity dependence on CO2 concentration. M–S and Fick diffusivities of CO2 are calculated by MD for the first time, both of which increase with increasing CO2 and H2O concentration and temperature. Based on self-diffusivity and M–S diffusivity, a quantity representing the coupling strength between CO2 molecules is presented; it increases firstly with CO2 concentration but begins to decrease when CO2 concentration is beyond 2.
Electron-transfer chain in respiratory complex I
Authors: Martin Daniel R. , Matyushov Dmitry V. 
Published: July 2017

AbstractComplex I is a part of the respiration energy chain converting the redox energy into the cross-membrane proton gradient. The electron-transfer chain of iron-sulfur cofactors within the water-soluble peripheral part of the complex is responsible for the delivery of electrons to the proton pumping subunit. The protein is porous to water penetration and the hydration level of the cofactors changes when the electron is transferred along the chain. High reaction barriers and trapping of the electrons at the iron-sulfur cofactors are prevented by the combination of intense electrostatic noise produced by the protein-water interface with the high density of quantum states in the iron-sulfur clusters caused by spin interactions between paramagnetic iron atoms. The combination of these factors substantially lowers the activation barrier for electron transfer compared to the prediction of the Marcus theory, bringing the rate to the experimentally established range. The unique role of iron-sulfur clusters as electron-transfer cofactors is in merging protein-water fluctuations with quantum-state multiplicity to allow low activation barriers and robust operation. Water plays a vital role in electron transport energetics by electrowetting the cofactors in the chain upon arrival of the electron. A general property of a protein is to violate the fluctuation-dissipation relation through nonergodic sampling of its landscape. High functional efficiency of redox enzymes is a direct consequence of nonergodicity.
Endothelial cells by inactivation of VHL gene direct angiogenesis, not vasculogenesis via Twist1 accumulation associated with hemangioblastoma neovascularization
Authors: Wang Ying , Chen Dan-Qi , Chen Ming-Yu , Ji Kai-Yuan , Ma De-Xuan , Zhou Liang-Fu 
Published: July 2017

AbstractInactivation of the VHL tumour suppressor gene is a highly frequent genetic event in the carcinogenesis of central nervous system-(CNS) hemangioblastomas (HBs). The patterning of the similar embryonic vasculogenesis is an increasing concern in HB-neovascularization, and the classic vascular endothelial growth factor (VEGF)-mediated angiogenesis driven by VHL loss-of-function from human endothelium have been questioned. With this regard, we identify a distinct, VHL silencing-driven mechanism in which human vascular endothelial cells by means of increasing cell proliferation and decreasing cell apoptosis, is concomitant with facilitating accumulation of Twist1 protein in vascular endothelial cells in vitro. Importantly, this molecular mechanism is also pinpointed in CNS-HBs, and associated with the process of HB-neovascularization. In contrast with recent studies of HB-neovascularization, these modified cells did not endow with the typical features of vasculogenesis, indicating that this is a common angiogenesis implementing the formation of the vascular network. Taken together, these findings suggest that vasculogenesis and angiogenesis may constitute complementary mechanisms for HB-neovascularization, and could provide a rational recognition of single anti-angiogenic intervention including targeting to the Twist1 signalling for HBs.
Methyl-CpG binding domain proteins inhibit interspecies courtship and promote aggression in Drosophila
Authors: Gupta Tarun , Morgan Hannah R. , Andrews Jonathan C. , Brewer Edmond R. , Certel Sarah J. 
Published: July 2017

AbstractReproductive isolation and speciation are driven by the convergence of environmental and genetic variation. The integration of these variation sources is thought to occur through epigenetic marks including DNA methylation. Proteins containing a methyl-CpG-binding domain (MBD) bind methylated DNA and interpret epigenetic marks, providing a dynamic yet evolutionarily adapted cellular output. Here, we report the Drosophila MBD-containing proteins, dMBD-R2 and dMBD2/3, contribute to reproductive isolation and survival behavioral strategies. Drosophila melanogaster males with a reduction in dMBD-R2 specifically in octopamine (OA) neurons exhibit courtship toward divergent interspecies D. virilis and D. yakuba females and a decrease in conspecific mating success. Conspecific male-male courtship is increased between dMBD-R2-deficient males while aggression is reduced. These changes in adaptive behavior are separable as males with a hypermethylated OA neuronal genome exhibited a decrease in aggression without altering male-male courtship. These results suggest Drosophila MBD-containing proteins are required within the OA neural circuitry to inhibit interspecies and conspecific male-male courtship and indicate that the genetically hard-wired neural mechanisms enforcing behavioral reproductive isolation include the interpretation of the epigenome.
Pathological effect of arterial ischaemia and venous congestion on rat testes
Authors: Hirai Shuichi , Hatayama Naoyuki , Naito Munekazu , Nagahori Kenta , Kawata Shinichi , Hayashi Shogo , Qu Ning , Terayama Hayato , Shoji Sunao , Itoh Masahiro 
Published: July 2017

AbstractMany studies on various organs have concluded that venous congestion (VC) causes severe organ dysfunction with elevation of oxidative stress relative to that of arterial ischaemia (AI). However, a comparison of the pathological effects of AI and VC on the testes has not been conducted. In this study, models of AI and VC and their reperfusion in rat testes, respectively, were developed and analysed. Testicular arteries or veins were interrupted for 6 h, re-perfused and kept for 4 weeks; the effects on the testes were then evaluated. Severe spermatogenic disturbances were observed at 4 weeks after reperfusion in AI but not in VC. At 6 h after blood flow interruption, oxidative stress was significantly increased and germ cells were severely damaged in AI compared with those in VC. RT-PCR analyses revealed that haem oxygenase-1, which exhibits anti-oxidative effects, and vascular endothelial growth factor-A, which exhibits vasculogenic effects, were significantly increased in VC but not in AI. Surprisingly, the results of our experiment in rat testes differed from those of experiments in previous studies performed in other organs. Oxidative stress in testes was more easily elevated by AI than it was by VC, explainable by the different experimental conditions.
Non-target effects on soil microbial parameters of the synthetic pesticide carbendazim with the biopesticides cantharidin and norcantharidin
Authors: Shao Hainan , Zhang Yalin 
Published: July 2017

AbstractConsidering the fact that biopesticides are increasingly used to replace synthetic pesticides in pest control, it is necessary to assess their ecotoxicity and especially their non-target effects on soil microorganisms, which is largely unknown. In this study, the effects of the synthetic pesticide carbendazim and the biopesticides (cantharidin and norcantharidin) on soil microbial parameters in a silt loam soil were evaluated. By using commercial formulations at the recommended and higher rates, both cantharidin and norcantharidin induced adverse effects on soil invertase, phosphatase activities and fungal gene structure, but these changes were transient. After about two weeks, the harmful effects owing to the application of pesticides phased out and eventually became comparable with non-treated samples. The degradation of cantharidin and norcantharidin was rapid and can be completed within a few days in the soil. None of the three pesticides caused significant shifts in urease activity. This study provides a comprehensive assessment of the soil microbial toxicity of these biopesticides for reasonable and efficient usage.
Factors affecting distribution patterns of organic carbon in sediments at regional and national scales in China
Authors: Cao Qingqing , Wang Hui , Zhang Yiran , Lal Rattan , Wang Renqing , Ge Xiuli , Liu Jian 
Published: July 2017

AbstractWetlands are an important carbon reservoir pool in terrestrial ecosystems. Light fraction organic carbon (LFOC), heavy fraction organic carbon (HFOC), and dissolved organic carbon (DOC) were fractionated in sediment samples from the four wetlands (ZR: Zhaoniu River; ZRCW: Zhaoniu River Constructed Wetland; XR: Xinxue River; XRCW: Xinxue River Constructed Wetland). Organic carbon (OC) from rivers and coasts of China were retrieved and statistically analyzed. At regional scale, HFOC stably dominates the deposition of OC (95.4%), whereas DOC and LFOC in ZR is significantly higher than in ZRCW. Concentration of DOC is significantly higher in XRCW (30.37 mg/l) than that in XR (13.59 mg/l). DOC and HFOC notably distinguish between two sampling campaigns, and the deposition of carbon fractions are limited by low nitrogen input. At the national scale, OC attains the maximum of 2.29% at precipitation of 800 mm. OC has no significant difference among the three climate zones but significantly higher in river sediments than in coasts. Coastal OC increases from Bohai Sea (0.52%) to South Sea (0.70%) with a decrease in latitude. This study summarizes the factors affecting organic carbon storage in regional and national scale, and have constructive implications for carbon assessment, modelling, and management.
MEN1/Menin regulates milk protein synthesis through mTOR signaling in mammary epithelial cells
Authors: Li Honghui , Liu Xue , Wang Zhonghua , Lin Xueyan , Yan Zhengui , Cao Qiaoqiao , Zhao Meng , Shi Kerong 
Published: July 2017

AbstractThe MEN1 gene, which encodes the protein Menin, was investigated for its regulatory role in milk protein synthesis in mammary glands. Menin responds to nutrient and hormone levels via the PI3K/Akt/mTOR pathway. Bovine mammary epithelial cells and tissues were used as experimental models in this study. The results revealed that the milk protein synthesis capacity of mammary epithelial cells could be regulated by MEN1/Menin. The overexpression of Menin caused significant suppression of factors involved in the mTOR pathway, as well as milk protein κ-casein (CSNK). In contrast, a significant increase in these factors and CSNK was observed upon MEN1/Menin knockdown. The repression of MEN1/Menin on the mTOR pathway was also observed in mammary gland tissues. Additionally, MEN1/Menin was found to elicit a negative response on prolactin (PRL) and/or insulin (INS), which caused a similar downstream impact on mTOR pathway factors and milk proteins. Collectively, our data indicate that MEN1/Menin could play a regulatory role in milk protein synthesis through mTOR signaling in the mammary gland by mediating the effects of hormones and nutrient status. The discovery of Menin’s role in mammary glands suggests Menin could be potential new target for the improvement of milk performance and adjustment of lactation period of dairy cows.
Mercury evidence for pulsed volcanism during the end-Triassic mass extinction
Authors: Percival Lawrence M. E. , Ruhl Micha , Hesselbo Stephen P. , Jenkyns Hugh C. , Mather Tamsin A. , Whiteside Jessica H. 
Published: July 2017

Significance
The end of the Triassic Period (∼201.5 million years ago) witnessed one of the largest mass extinctions of animal life known from Earth history. This extinction is suggested to have coincided with and been caused by one of the largest known episodes of volcanic activity in Earth’s history. This study examines mercury concentrations of sediments from around the world that record this extinction. Mercury is emitted in gaseous form during volcanism, and subsequently deposited in sediments. We find numerous pulsed elevations of mercury concentrations in end-Triassic sediments. These peaks show that the mass extinction coincided with large-scale, episodic, volcanism. Such episodic volcanism likely perturbed the global environment over a long period of time and strongly delayed ecological recovery.
UCP1 deficiency causes brown fat respiratory chain depletion and sensitizes mitochondria to calcium overload-induced dysfunction
Authors: Kazak Lawrence , Chouchani Edward T. , Stavrovskaya Irina G. , Lu Gina Z. , Jedrychowski Mark P. , Egan Daniel F. , Kumari Manju , Kong Xingxing , Erickson Brian K. , Szpyt John , Rosen Evan D. , Murphy Michael P. , Kristal Bruce S. , Gygi Steven P. , Spiegelman Bruce M. 
Published: July 2017

Significance
We describe a physiological role for uncoupling protein 1 (UCP1) in the regulation of reactive oxygen species. Notably, the molecular differences between brown fat mitochondria from wild-type and UCP1 knockout (UCP1-KO) mice extend substantially beyond the deletion of UCP1 itself. Thus, caution must be taken when attributing a brown fat phenotype solely to UCP1 deletion when these animals are used. Given the wide utilization of the UCP1-KO mouse model, these data are of critical importance for the scientific communities studying obesity, thermogenesis and energy metabolism, and mitochondrial biology.
Development and molecular characterization of wheat-Aegilops peregrinaIntrogression Lines with resistance to leaf rust and stripe rust
Authors: Narang Deepika , Kaur Satinder , Saini Jyoti , Chhuneja Parveen 
Published: July 2017

AbstractA wild non-progenitor species from wheat tertiary gene poolAegilops peregrinaaccession pau3519 (UUSS) was used for introgression of leaf rust and stripe rust resistance in bread wheat. It was crossed and backcrossed with hexaploid wheat line Chinese SpringPhIto develop two homozygous BC2F6wheat-Ae. peregrinaintrogression lines (ILs) viz. IL pau16058 and IL pau16061 through induced homoeologous recombination. Homozygous lines were screened against sixPuccinia triticinaand twoPuccinia striiformisf. sp.triticipathotypes at the seedling stage and a mixture of prevalent pathotypes of both rust pathogens at the adult plant stage. IL pau16061 showed resistance to leaf rust only while IL pau16058 was resistant to both leaf and stripe rust pathotypes throughout plant life. Molecular characterization of these ILs aided in defining the introgressed regions. Identification of linked markers with advance genomic technologies will aid in marker assisted pyramiding of alien genes in cultivated wheat background.
Investigating termite nest thermodynamics using a quick-look method and the heat equation
Authors: Gouttefarde Rémi , Bon Richard , Fourcassié Vincent , Arrufat Patrick , Haifig Ives , Baehr Christophe , Jost Christian 
Published: July 2017

AbstractTermite mounds are often cited as an example of efficient thermoregulated structures. Nest thermal stability can be critical for insects that are particularly sensitive to heat and desiccation. Few studies have measured internal temperature of termite nests with respect to environmental parameters, especially in Neotropical species. In this study, we analyzed the thermal profiles of different parts ofProcornitermes araujoinests, a neotropical mound-building termite of the Braziliancerrado. To read into our dataset we first used rasterization, a method that allows a quick-look assessment of time-series. Our results show that nest architecture efficiently buffers against environmental temperature fluctuations while at the same time maintaining a relatively high internal temperature in the core. This rather stable internal climate follows nevertheless the external temperature long-term averages. Using a novel numerical scheme, we further show that the heat transfer dynamics are well described by the classical heat equation, with an additional heat source whose origin is discussed.
Automated Parameterization of Predictive Kinetic Metabolic Models from Sparse Datasets for Efficient Optimization of Many-Enzyme Heterologous Pathways
Authors: Halper Sean M. , Farasat Iman , Salis Howard M. 
Published: July 2017

AbstractEngineered heterologous metabolic pathways can convert low-cost feedstock into high-value products, though it remains a significant challenge to reliably and efficiently maximize end-product biosynthesis, particularly when many enzymes must be co-expressed together. When current approaches are applied to many-enzyme pathways, the construction and characterization process is highly iterative and laborious, while generating high-dimensional datasets that remain difficult to analyze for forward engineering efforts. To overcome these challenges, we developed a new algorithm that determines the highly non-linear and high-dimensional relationship between a pathway’s enzyme expression levels and its end-product productivity from common characterization of a small number of heterologous pathway variants. We combined kinetic metabolic modeling, elementary mode analysis, model reduction, de-dimensionalization, and genetic algorithm optimization into an automated procedure that parameterizes accurate kinetic metabolic models from sparsely characterized pathway variant libraries with varied enzyme expression levels. The resulting Pathway Maps are used to determine rate-limiting steps, predict optimal expression levels, identify allosteric interactions, rank-order enzyme kinetics, and prioritize protein engineering efforts. We demonstrate the Pathway Map Calculator algorithm on two experimental datasets, a 3-enzyme carotenoid biosynthesis pathway and a 9-enzyme limonene biosynthesis pathway, as well as a series ofin silicopathway examples to rigorously demonstrate the algorithm’s accuracy, linear scaling, and high tolerance to measurement noise. By greatly reducing experimental efforts and providing quantitative forward engineering predictions, the Pathway Map Calculator has the potential to dramatically accelerate the engineering of many-enzyme heterologous metabolic pathways.HighlightsWe developed an automated algorithm that uses a small number of characterized pathway variants to determine the pathway’s expression-productivity relationship.The Pathway Map Calculator is accurate, scales linearly on many-enzyme pathways, distinguishes allosteric interactions, and tolerates substantial measurement noise.Pathway Maps are used to predict optimal enzyme expression levels, identify rate-limiting steps, and prioritize protein engineering efforts
Understanding the relationship between the economy and crime: Canadian provinces, 1981-2009
Authors: Jalles Joao Tovar , Andresen Martin A. 
Published: July 2017

PurposeThe purpose of this paper is to investigate the importance of multiple measures of the economy while investigating the role of the economy with crime, as well as the sensitivity of those results.Design/methodology/approachProvincial-level data, 1981-2009, and a series of statistical specifications.FindingsThe authors find overall support for the Cantor and Land’s (1985) model of unemployment and crime. The authors are also able to show the importance of considering multiple measures of economic activity and multiple statistical methods of analysis for the sensitivity of results.Originality/valuePrevious research has shown the importance of multiple measures of the economy but not multiple statistical methods as a sensitivity analysis. The authors provide such a sensitivity analysis and show that the Cantor and Land’s (1985) model has significant support.