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1. chinaXiv:202006.00230 [pdf]

Tree ring based drought variability in Northwest Tajikistan since 1895 AD

YANG Meilin; YU Yang; ZHANG Haiyan; WANG Qian; GAN Miao; YU Ruide
Subjects: Geosciences >> History of Geosciences

Determining the mechanisms controlling the changes of wet and dry conditions will improve our understanding of climate change over the past hundred years, which is of great significance to the study of climate and environmental changes in the arid regions of Central Asia. Forest trees are ecologically significant in the local environment, and therefore the tree ring analysis can provide a clear record of regional historical climate. This study analyzed the correlation between the tree ring width chronology of Juniperus turkestanica Komarov and the standardized precipitation evapotranspiration index (SPEI) in Northwest Tajikistan, based on 56 tree ring samples collected from Shahristan in the Pamir region. Climate data including precipitation, temperature and the SPEI were downloaded from the Climate Research Unit (CRU) TS 4.00. The COFECHA program was used for cross-dating, and the ARSTAN program was used to remove the growth trend of the tree itself and the influence of non-climatic factors on the growth of the trees. A significant correlation was found between the radial growth of J. turkestanica trees and the monthly mean SPEI of February–April. The monthly mean SPEI sequence of February–April during the period of 1895–2016 was reconstructed, and the reconstruction equation explained 42.5% of the variance. During the past 122 a (1895–2016), the study area has experienced three wetter periods (precipitation above average): 1901–1919, 1945–1983 and 1995–2010, and four drier periods (precipitation below average): 1895–1900, 1920–1944, 1984–1994 and 2011–2016. The spatial correlation analysis revealed that the monthly mean SPEI reconstruction sequence of February–April could be used to characterize the large-scale dry-wet variations in Northwest Tajikistan during the period of 1895–2016. This study could provide comparative data for validating the projections of climate models and scientific basis for managing water resources in Tajikistan in the context of climate change.

submitted time 2020-06-22 From cooperative journals:《Journal of Arid Land》 Hits187Downloads92 Comment 0

2. chinaXiv:201901.00114 [pdf]

Climate change, water resources and sustainable development in the arid and semi-arid lands of Central Asia in the past 30 years

YU Yang; PI Yuanyue; YU Xiang
Subjects: Geosciences >> Geography

The countries of Central Asia are collectively known as the five ''-stans'': Uzbekistan, Kyrgyzstan, Turkmenistan, Tajikistan and Kazakhstan. In recent times, the Central Asian region has been affected by the shrinkage of the Aral Sea, widespread desertification, soil salinization, biodiversity loss, frequent sand storms, and many other ecological disasters. This paper is a review article based upon the collection, identification and collation of previous studies of environmental changes and regional developments in Central Asia in the past 30 years. Most recent studies have reached a consensus that the temperature rise in Central Asia is occurring faster than the global average. This warming trend will not only result in a higher evaporation in the basin oases, but also to a significant retreat of glaciers in the mountainous areas. Water is the key to sustainable development in the arid and semi-arid regions in Central Asia. The uneven distribution, over consumption, and pollution of water resources in Central Asia have caused severe water supply problems, which have been affecting regional harmony and development for the past 30 years. The widespread and significant land use changes in the 1990s could be used to improve our understanding of natural variability and human interaction in the region. There has been a positive trend of trans-border cooperation among the Central Asian countries in recent years. International attention has grown and research projects have been initiated to provide water and ecosystem protection in Central Asia. However, the agreements that have been reached might not be able to deliver practical action in time to prevent severe ecological disasters. Water management should be based on hydrographic borders and ministries should be able to make timely decisions without political intervention. Fully integrated management of water resources, land use and industrial development is essential in Central Asia. The ecological crisis should provide sufficient motivation to reach a consensus on unified water management throughout the region.

submitted time 2019-01-17 From cooperative journals:《Journal of Arid Land》 Hits3682Downloads557 Comment 0

3. chinaXiv:201803.00010 [pdf]

Model based decision support system for land use changes and socio-economic assessments

YU, Yang; CHEN, Xi; HUTTNER, Philipp; HINNENTHAL, Marie; BRIEDEN, Andreas; SUN, Lingxiao; DSE, ISMarkus
Subjects: Physics >> General Physics: Statistical and Quantum Mechanics, Quantum Information, etc.

Hydrological models are often linked with other models in cognate sciences to understand the interactions among climate, earth, water, ecosystem, and human society. This paper presents the development and implementation of a decision support system (DSS) that links the outputs of hydrological models with real-time decision making on social-economic assessments and land use management. Discharge and glacier geometry changes were simulated with hydrological model, water availability in semi-arid environments. Irrigation and ecological water were simulated by a new commercial software MIKE HYDRO. Groundwater was simulated by MODFLOW. All the outputs of theses hydrological models were taken as inputs into the DSS in three types of links: regression equations, stationary data inputs, or dynamic data inputs as the models running parallel in the simulation periods. The DSS integrates the hydrological data, geographic data, social and economic statistical data, and establishes the relationships with equations, conditional statements and fuzzy logics. The programming is realized in C++. The DSS has four remarkable features: (1) editable land use maps to assist decision-making; (2) conjunctive use of surface and groundwater resources; (3) interactions among water, earth, ecosystem, and humans; and (4) links with hydrological models. The overall goal of the DSS is to combine the outputs of scientific models, knowledge of experts, and perspectives of stakeholders, into a computer-based system, which allows sustainability impact assessment within regional planning; and to understand ecosystem services and integrate them into land and water management.

submitted time 2018-02-28 From cooperative journals:《Journal of Arid Land》 Hits1387Downloads679 Comment 0

4. chinaXiv:201605.01808 [pdf]

Significant Expansion of Fluorescent Protein Sensing Ability through the Genetic Incorporation of Superior Photo-Induced Electron-Transfer Quenchers

Liu, Xiaohong; Jiang, Li; Li, Jiasong; Wang, Li; Zhou, Qing; Lv, Xiaoxuan; Gong, Weimin; Wang, Jiangyun; Lu, Yi; Lu, Yi; Yu, Yang
Subjects: Biology >> Biophysics

Photo-induced electron transfer (PET) is ubiquitous for photosynthesis and fluorescent sensor design. However, genetically coded PET sensors are underdeveloped, due to the lack of methods to site-specifically install PET probes on proteins. Here we describe a family of acid and Mn(III) turn-on fluorescent protein (FP) sensors, named iLovU, based on PET and the genetic incorporation of superior PET quenchers in the fluorescent flavoprotein iLov. Using the iLovU PET sensors, we monitored the cytoplasmic acidification process, and achieved Mn(III) fluorescence sensing for the first time. The iLovU sensors should be applicable for studying pH changes in living cells, monitoring biogentic Mn(III) in the environment, and screening for efficient manganese peroxidase, which is highly desirable for lignin degradation and biomass conversion. Our work establishes a platform for many more protein PET sensors, facilitates the de novo design of metalloenzymes harboring redox active residues, and expands our ability to probe protein conformational dynamics.

submitted time 2016-05-18 Hits2468Downloads941 Comment 0

5. chinaXiv:201605.01531 [pdf]

Defining the Role of Tyrosine and Rational Tuning of Oxidase Activity by Genetic Incorporation of Unnatural Tyrosine Analogs

Lv, Xiaoxuan; Li, Jiasong; Zhou, Qing; Wang, Jiangyun; Lv, Xiaoxuan; Li, Jiasong; Zhou, Qing; Wang, Jiangyun; Yu, Yang; Lu, Yi; Cui, Chang; Mukherjee, Arnab; Lu, Yi; Hosseinzadeh, Parisa; Lu, Yi; Nilges, Mark J.
Subjects: Biology >> Biophysics

While a conserved tyrosine (Tyr) is found in oxidases, the roles of phenol ring pK(a) and reduction potential in O-2 reduction have not been defined despite many years of research on numerous oxidases and their models. These issues represent major challenges in our understanding of O-2 reduction mechanism in bioenergetics. Through genetic incorporation of unnatural amino acid analogs of Tyr, with progressively decreasing pKa of the phenol ring and increasing reduction potential, in the active site of a functional model of oxidase in myoglobin, a linear dependence of both the O-2 reduction activity and the fraction of H2O formation with the pKa of the phenol ring has been established. By using these unnatural amino acids as spectroscopic probe, we have provided conclusive evidence for the location of a Tyr radical generated during reaction with H2O2, by the distinctive hyperfine splitting patterns of the halogenated tyrosines and one of its deuterated derivatives incorporated at the 33 position of the protein. These results demonstrate for the first time that enhancing the proton donation ability of the Tyr enhances the oxidase activity, allowing the Tyr analogs to augment enzymatic activity beyond that of natural Tyr.

submitted time 2016-05-12 Hits1220Downloads612 Comment 0

6. chinaXiv:201605.01485 [pdf]

Synthetic Model of the Oxygen-Evolving Center: Photosystem II under the Spotlight

Hu, Cheng; Liu, Xiaohong; Wang, Jiangyun; Yu, Yang
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

The oxygen-evolving center (OEC) in photosystem II catalyzes a water splitting reaction. Great efforts have already been made to artificially synthesize the OEC, in order to elucidate the structure-function relationship and the mechanism of the reaction. Now, a new synthetic model makes the best mimic yet of the OEC. This recent study opens up the possibility to study the mechanism of photosystem II and photosynthesis in general for applications in renewable energy and synthetic biology.

submitted time 2016-05-12 Hits1024Downloads473 Comment 0

7. chinaXiv:201605.01451 [pdf]

A Designed Metalloenzyme Achieving the Catalytic Rate of a Native Enzyme

Liu, Xiaohong; Wang, Jiangyun; Yu, Yang; Lu, Yi; Cui, Chang; Petrik, Igor D.; Lu, Yi
Subjects: Biology >> Biophysics

Terminal oxidases catalyze four-electron reduction of oxygen to water, and the energy harvested is utilized to drive the synthesis of adenosine triphosphate. While much effort has been made to design a catalyst mimicking the function of terminal oxidases, most biomimetic catalysts have much lower activity than native oxidases. Herein we report a designed oxidase in myoglobin with an O-2 reduction rate (52 s(-1)) comparable to that of a native cytochrome (cyt) cbb(3) oxidase (SO s(-1)) under identical conditions. We achieved this goal by engineering more favorable electrostatic interactions between a functional oxidase model designed in sperm whale myoglobin and its native redox partner, cyt b(5), resulting in a 400-fold electron transfer (ET) rate enhancement. Achieving high activity equivalent to that of native enzymes in a designed metalloenzyme offers deeper insight into the roles of tunable processes such as ET in oxidase activity and enzymatic function and may extend into applications such as more efficient oxygen reduction reaction catalysts for biofuel cells.

submitted time 2016-05-12 Hits721Downloads418 Comment 0

8. chinaXiv:201605.01346 [pdf]

Genetic Incorporation of N-epsilon-Formyllysine, a New Histone Post-translational Modification

Wang, Tianyuan; Yin, Xuebin; Zhou, Qing; Li, Fahui; Wang, Jiangyun; Yu, Yang; Yin, Xuebin
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

Lysine formylation is a newly discovered post-translational modification (PTM) in histones and other nuclear proteins; it has a well-recognized but poorly defined role in chromatin conformation modulation and gene expression. To date, there is no general method to site-specifically incorporate N-epsilon-formyllysine at a defined site of a protein. Here we report the highly efficient genetic incorporation of the unnatural amino acid N-epsilon-formyllysine into proteins produced in Escherichia coli and mammalian cells, by using an orthogonal N-epsilon-formyllysine tRNAsynthetase/tRNA(CUA) pair. This technique can be applied to study the role of lysine formylation in epigenetic regulation.

submitted time 2016-05-11 Hits567Downloads332 Comment 0

9. chinaXiv:201605.01273 [pdf]

Ultrafast Photoinduced Electron Transfer in Green Fluorescent Protein Bearing a Genetically Encoded Electron Acceptor

Lv, Xiaoxuan; Hu, Cheng; Gao, Feng; Li, Jiasong; Liu, Xiaohong; Deng, Kai; Zheng, Peng; Gong, Weimin; Wang, Jiangyun; Lv, Xiaoxuan; Hu, Cheng; Gao, Feng; Li, Jiasong; Liu, Xiaohong; Deng, Kai; Zheng, Peng; Gong, Weimin; Wang, Jiangyun; Zhou, Meng; Xia, Andong
Subjects: Biology >> Biophysics

Electron transfer (ET) is widely used for driving the processes that underlie the chemistry of life. However, our abilities to probe electron transfer mechanisms in proteins and design redox enzymes are limited, due to :the lack of methods to site-specifically insert electron acceptors into proteins in vivo. Here we describe the synthesis and genetic incorporation of 4-fluoro-3-nitrophenylalanine (FNO(2)Phe), which has similar reduction potentials to NAD(P)H and ferredoxin, the most important biological reductants. Through the genetic incorporation of FNO2Phe into green fluorescent:protein (GFP) and femtosecond transient absorption measurement, we show that photoinduced electron transfer (PET) from the GFP chromophore to FNO2Phe occurs very fast (within 11 ps), which is comparable to that of the first electron transfer step in photosystem I, from P700* to A(0). This genetically encoded, low-reduction potential unnatural amino acid (UAA) can significantly in-Trove our ability to investigate electron transfer mechanisms in complex reductases and facilitate the design of miniature proteins that mimic their functions.

submitted time 2016-05-11 Hits743Downloads419 Comment 0

10. chinaXiv:201605.00772 [pdf]

Modeling xeroderma pigmentosum associated neurological pathologies with patients-derived iPSCs

Fu, Lina; Xu, Xiuling; Ren, Ruotong; Zhang, Weiqi; Yang, Jiping; Ren, Xiaoqing; Wang, Si; Zhao, Yang; Liu, Guang-Hui; Ren, Ruotong; Zhang, Weiqi; Liu, Guang-Hui; Qu, Jing; Wu, Jun; Belmonte, Juan Carlos Izpisua; Wu, Jun; Sun, Liang; Yang, Ze; Yu, Yang; Qiao, Jie
Subjects: Biology >> Biophysics >> Cell Biology

Xeroderma pigmentosum (XP) is a group of genetic disorders caused by mutations of XP-associated genes, resulting in impairment of DNA repair. XP patients frequently exhibit neurological degeneration, but the underlying mechanism is unknown, in part due to lack of proper disease models. Here, we generated patient-specific induced pluripotent stem cells (iPSCs) harboring mutations in five different XP genes including XPA, XPB, XPC, XPG, and XPV. These iPSCs were further differentiated to neural cells, and their susceptibility to DNA damage stress was investigated. Mutation of XPA in either neural stem cells (NSCs) or neurons resulted in severe DNA damage repair defects, and these neural cells with mutant XPA were hyper-sensitive to DNA damage-induced apoptosis. Thus, XP-mutant neural cells represent valuable tools to clarify the molecular mechanisms of neurological abnormalities in the XP patients.

submitted time 2016-05-05 Hits802Downloads451 Comment 0

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