分类: 生物学 >> 植物学 >> 植物生态学和植物地理学 提交时间: 2016-06-13
摘要: 在全球气候变化背景下, 未来我国北方半干旱地区的降水格局将呈现出季节与年际间降水波动增强和极端降水事件增加的趋势。水分是半干旱草原的主要限制因子, 降水格局变化导致的土壤水分状况的改变必然对生态系统的结构和功能产生显著的影响。该研究选取内蒙古多伦、锡林浩特两个典型半干旱草原群落, 通过分析2006–2013年的降水和多层次(0–10 cm、10 cm、20 cm、30 cm和50 cm)土壤含水量连续观测数据, 研究降水格局变化对土壤水分状况及其垂直分布的影响, 特别是土壤水分对降水事件的脉冲响应过程。结果表明: 两个站点的土壤含水量均呈现显著的季节及年际间波动, 其中, 深层水分波动相对较小, 表层水分波动相对剧烈。锡林浩特50 cm深处土壤含水量波动较大, 主要由于春季融雪对深层水分的补充。年际间多伦和锡林浩特生长季表层土壤含水量与降水量存在显著的正相关关系, 下层土壤含水量与降水量相关性不显著。研究发现最小2 mm的降水事件能够引起两个站点表层土壤含水量的升高, 即该地区有效降水为日降水量>2 mm。表层土壤含水量对独立降水事件的脉冲响应可通过一个指数方程很好地拟合出来。降水事件的大小决定了雨后表层土壤含水量的最大增量和持续时间, 同时这个脉冲响应过程还受到雨前土壤含水量的影响, 但该过程中并未发现植被因子(叶面积指数)的显著影响。降水后水分下渗深度及该深度的土壤含水量增量主要由降水事件大小主导, 同时受到雨前土壤含水量的影响。在多伦和锡林浩特, 平均每增加1 mm降水, 下渗深度分别增加1.06和0.79 cm。由此我们认为, 在内蒙古半干旱草原, 降水事件大小和雨前土壤干湿状况是影响土壤水分对降水响应的主要因素, 而植被因子的影响较小。
分类: 生物学 >> 生物物理学 >> 神经科学 提交时间: 2016-06-06
摘要: Previous studies have shown that the Hippo pathway effector yes-associated protein (YAP) plays an important role in maintaining stem cell proliferation. However, the precise molecular mechanism of YAP in regulating murine embryonic neural stem cells (NSCs) remains largely unknown. Here, we show that bone morphogenetic protein-2 (BMP2) treatment inhibited the proliferation of mouse embryonic NSCs, that YAP was critical for mouse NSC proliferation, and that BMP2 treatment-induced inhibition of mouse NSC proliferation was abrogated by YAP knockdown, indicating that the YAP protein mediates the inhibitory effect of BMP2 signaling. Additionally, we found that BMP2 treatment reduced YAP nuclear translocation, YAP-TEAD interaction, and YAP-mediated transactivation. BMP2 treatment inhibited YAP/TEAD-mediated Cyclin D1 (ccnd1) expression, and knockdown of ccnd1 abrogated the BMP2-mediated inhibition of mouse NSC proliferation. Mechanistically, we found that Smad1/4, effectors of BMP2 signaling, competed with YAP for the interaction with TAED1 and inhibited YAP's cotranscriptional activity. Our data reveal mechanistic cross talk between BMP2 signaling and the Hippo-YAP pathway in murine NSC proliferation, which may be exploited as a therapeutic target in neurodegenerative diseases and aging.
分类: 生物学 >> 植物学 >> 植物学研究、实验与植物演化、发展 提交时间: 2016-05-31
摘要: Grassland agriculture is experiencing a number of threats including declining profitability and loss of area to other land uses including expansion of the built environment as well as from cropland and forestry. The use of grassland as a natural resource either in terms of existing vegetation and land cover or planting of new species for bioenergy and other nonfood applications presents an opportunity, and potential solution, to maintain the broader ecosystem services that perennial grasslands provide as well as to improve the options for grassland farmers and their communities. This paper brings together different grass or grassland-based studies and considers them as part of a continuum of strategies that, when also combined with improvements in grassland production systems,will improve the overall efficiency of grasslands as an important natural resource and enable a greater area to be managed, replanted or conserved. These diversification options relate to those most likely to be available to farmers and land owners in the marginally economic or uneconomic grasslands of middle to northern Europe and specifically in the UK. Grasslands represent the predominant global land use and so these strategies are likely to be relevant to other areas although the grass species used may vary. The options covered include the use of biomass derived from the management of grasses in the urban and semi urban environment, semi-natural grassland systems as part of ecosystem management, pasture in addition to livestock production, and the planting and cropping of dedicated energy grasses. The adoption of such approaches would not only increase income from economically marginal grasslands, but would also mitigate greenhouse gas emissions from livestock production and help fund conservation of these valuable grassland ecosystems and landscapes, which is increasingly becoming a challenge.
分类: 生物学 >> 植物学 >> 植物学研究、实验与植物演化、发展 提交时间: 2016-05-31
摘要: A key global 21st century challenge is to maximize agricultural production while minimizing use of resources such as land, water, and energy to meet rising demand for produce. To meet this challenge, while also adapting to climate change, agriculture will have to become more knowledge intensive and deploy smarter farming techniques. The intention of this study was to: (1)Highlight the opportunity for web-based knowledge exchange to increase farm productivity and thus contribute to achieving food and energy security, (2) Give some examples of online farming information services such as the “CROPROTECT” tool I am developing in the UK, the CABI “Plantwise” Knowledge Bank and the IRRI “Rice Doctor,” and (3) Consider lessons learnt so far.There are huge opportunities to facilitate knowledge exchange through online systems for farmers and people who advise farmers. CROPROTECT is interacting with users to determine priorities in terms of the pests, weeds, and diseases covered and is providing key information to assist with their management. Knowledge is a critical input for farming systems. Crop protection in particular is becoming more difficult due to evolution of pest resistance and changes in legislation.Up to date information can be made rapidly available and shared online through websites and smartphone Apps. Agricultural extension no longer relies solely on physical meetings and printed documents. The capacity to share information via the Internet is tremendous with its potential to reach a wide audience in the farming community, to provide rapid updates and to interact more with the users. However, in an era of information deluge,accessing relevant information and ensuring reliability are essential considerations. There is also a need to bring science and farming communities together to turn information into relevant farming knowledge.
分类: 生物学 >> 植物学 >> 植物生态学和植物地理学 提交时间: 2016-05-30
摘要: Flood and drought are the two most prevalent abiotic stresses causing major yield reduction globally. In the last decade, molecular mechanisms of flood tolerance in rice have been revealed with successful release of flash flood-tolerant varieties to farmers. However, despite extensive research, the breakthrough of drought tolerance is still to come. In this review, we have examined the distribution and population types of drought-and flood-tolerant rice accessions, synthesized recent progresses of flood and drought tolerance research, and proposed a hypothesis that the molecular mechanisms of both drought and flood tolerance may be regulated by cross-talked pathways and coexist in aus subpopulation.We conclude that it is the time to mine the key regulator(s) of drought tolerance through de novo assembly of drought-tolerant aus landrace(s) with other molecular approaches and develop drought-tolerant rice using genome manipulation weaponry.
分类: 生物学 >> 植物学 >> 植物学研究、实验与植物演化、发展 提交时间: 2016-05-27
摘要: S.S.Z. performed the research with the help of L.S., X.D. and S.J.L. W.T. supervised the bioinformatics analysis. S.S.Z. and J.X.L. designed the experiment, analyzed the data and wrote the manuscript.
分类: 生物学 >> 植物学 >> 植物生态学和植物地理学 提交时间: 2016-05-27
分类: 生物学 >> 生物物理学 >> 神经科学 提交时间: 2016-05-18
摘要: Crowding, the identification difficulty for a target in the presence of nearby flankers, is ubiquitous in spatial vision and is considered a bottleneck of object recognition and visual awareness. Despite its significance, the neural mechanisms of crowding are still unclear. Here, we performed event-related potential and fMRI experiments to measure the cortical interaction between the target and flankers in human subjects. We found that the magnitude of the crowding effect was closely associated with an early suppressive cortical interaction. The cortical suppression was reflected in the earliest event-related potential component (C1), which originated in V1, and in the BOLD signal in V1, but not other higher cortical areas. Intriguingly, spatial attention played a critical role in the manifestation of the suppression. These findings provide direct and converging evidence that attention-dependent V1 suppression contributes to crowding at a very early stage of visual processing.
分类: 生物学 >> 生物物理学 >> 生物物理、生物化学与分子生物学 提交时间: 2016-05-18
摘要: Autophagosome formation is promoted by the PI3 kinase complex and negatively regulated by myotubularin phosphatases, indicating that regulation of local phosphatidylinositol 3-phosphate (PtdIns3P) levels is important for this early phase of autophagy. Here, we show that the Caenorhabditis elegans myotubularin phosphatase MTM-3 catalyzes PtdIns3P turnover late in autophagy. MTM-3 acts downstream of the ATG-2/EPG-6 complex and upstream of EPG-5 to promote autophagosome maturation into autolysosomes. MTM-3 is recruited to autophagosomes by PtdIns3P, and loss of MTM-3 causes increased autophagic association of ATG-18 in a PtdIns3P-dependent manner. Our data reveal critical roles of PtdIns3P turnover in autophagosome maturation and/or autolysosome formation.
分类: 生物学 >> 生物物理学 >> 肿瘤学 提交时间: 2016-05-15
摘要: Tumor necrosis factor receptor-associated protein 1 (TRAP1) is abnormally expressed in many cancers. In this study, we showed that TRAP1 is aberrantly upregulated in breast tumors compared to control tissues. TRAP1 knockdown downregulates mitochondrial aerobic respiratory, sensitizes cells to lethal stimuli, and inhibited tumor growth in MDA-MB-231 and MCF-7 breast cancer cells in vivo. TRAP1 overexpression, however, enhances the capacity to cope with stress conditions. These evidences suggested that TRAP1 is required for tumorigenesis. We also found that TRAP1 regulates the mitochondrial morphology. Relatively lower TRAP1 levels are associated with the rod-shaped mitochondrial phenotype in invasive and metastatic MDA-MB-231 breast cancer cells; on the contrary, higher TRAP1 levels are associated with the tubular network-shaped mitochondrial phenotype in non-invasive MCF-7 cells. Interestingly, the expression of TRAP1 in human breast cancer specimens inversely correlates with tumor grade. Overexpression of TRAP1 in MDA-MB-231 cells causes mitochondrial fusion, triggers mitochondria to form tubular networks, and suppresses cell migration and invasion in vitro and in vivo. These data link TRAP1-regulated mitochondrial dynamics and function with tumorigenesis of breast cancer and suggested that TRAP1 may therefore be a potential target for breast cancer drug development.
分类: 生物学 >> 生物物理学 >> 免疫学 提交时间: 2016-05-15
摘要: The lineage commitment of HSCs generates balanced myeloid and lymphoid populations in hematopoiesis. However, the underlying mechanisms that control this process remain largely unknown. Here, we show that insulin-insulin receptor (InsR) signaling is required for lineage commitment of multipotent progenitors (MPPs). Deletion of Insr in murine bone marrow causes skewed differentiation of MPPs to myeloid cells. mTOR acts as a downstream effector that modulates MPP differentiation. mTOR activates Stat3 by phosphorylation at serine 727 under insulin stimulation, which binds to the promoter of Ikaros, leading to its transcription priming. Our findings reveal that the insulin-InsR signaling drives MPP differentiation into lymphoid lineages in early lymphopoiesis, which is essential for maintaining a balanced immune system for an individual organism.
分类: 生物学 >> 生物物理学 >> 生物物理、生物化学与分子生物学 提交时间: 2016-05-15
摘要: The cyclic nucleotide-binding (CNB)-like protein (CNB-L) from Brucella abortus shares sequence homology with CNB domain-containing proteins. We determined the crystal structure of CNB-L at 2.0 angstrom resolution in the absence of its C-terminal helix and nucleotide. The 3D structure of CNB-L is in a twofold symmetric form. Each protomer shows high structure similarity to that of cGMP-binding domain-containing proteins, and likely mimics their nucleotide-free conformation. A key residue, Glu17, mediates the dimerization and prevents binding of cNMP to the canonical ligand-pocket. The structurally observed dimer of CNB-L is stable in solution, and thus is likely to be biologically relevant. (C) 2015 Elsevier Inc. All rights reserved.
分类: 生物学 >> 生物物理学 >> 生物物理、生物化学与分子生物学 提交时间: 2016-05-15
摘要: Multicellular organisms have multiple homologs of the yeast ATG8 gene, but the differential roles of these homologs in autophagy during development remain largely unknown. Here we investigated structure/function relationships in the two C. elegans Atg8 homologs, LGG-1 and LGG-2. lgg-1 is essential for degradation of protein aggregates, while lgg-2 has cargo-specific and developmental-stage-specific roles in aggregate degradation. Crystallography revealed that the N-terminal tails of LGG-1 and LGG-2 adopt the closed and open form, respectively. LGG-1 and LGG-2 interact differentially with autophagy substrates and Atg proteins, many of which carry a LIR motif. LGG-1 and LGG-2 have structurally distinct substrate binding pockets that prefer different residues in the interacting LIR motif, thus influencing binding specificity. Lipidated LGG-1 and LGG-2 possess distinct membrane tethering and fusion activities, which may result from the N-terminal differences. Our study reveals the differential function of two ATG8 homologs in autophagy during C. elegans development.
分类: 生物学 >> 生物物理学 >> 生物物理、生物化学与分子生物学 提交时间: 2016-05-15
摘要: Insulin resistance and abdominal obesity are present in the majority of people with the metabolic syndrome. Antioxidant therapy might be a useful strategy for type 2 diabetes and other insulin-resistant states. The combination of vitamin C (Vc) and vitamin E has synthetic scavenging effect on free radicals and inhibition effect on lipid peroxidation. However, there are few studies about how to define the best combination of more than three anti-oxidants as it is difficult or impossible to test the anti-oxidant effect of the combination of every concentration of each ingredient experimentally. Here we present a math model, which is based on the classical Hill equation to determine the best combination, called Fixed Dose Combination (FDC), of several natural anti-oxidants, including Vc, green tea polyphenols (GTP) and grape seed extract proanthocyanidin (GSEP). Then we investigated the effects of FDC on oxidative stress, blood glucose and serum lipid levels in cultured 3T3-L1 adipocytes, high fat diet (HFD)-fed rats which serve as obesity model, and KK-ay mice as diabetic model. The level of serum malondialdehyde (MDA) in the treated rats was studied and Hematoxylin-Eosin (HE) staining or Oil red slices of liver and adipose tissue in the rats were examined as well. FDC shows excellent antioxidant and anti-glycation activity by attenuating lipid peroxidation. FDC determined in this investigation can become a potential solution to reduce obesity, to improve insulin sensitivity and be beneficial for the treatment of fat and diabetic patients. It is the first time to use the math model to determine the best ratio of three anti-oxidants, which can save much more time and chemical materials than traditional experimental method. This quantitative method represents a potentially new and useful strategy to screen all possible combinations of many natural anti-oxidants, therefore may help develop novel therapeutics with the potential to ameliorate the worldwide metabolic abnormalities. (C) 2015 The Authors. Published by Elsevier B.V.
分类: 生物学 >> 生物物理学 >> 细胞生物学 提交时间: 2016-05-15
摘要: GADD45A is a TP53-regulated and DNA damage-inducible tumor suppressor protein, which regulates cell cycle arrest, apoptosis, and DNA repair, and inhibits tumor growth and angiogenesis. However, the function of GADD45A in autophagy remains unknown. In this report, we demonstrate that GADD45A plays an important role in regulating the process of autophagy. GADD45A is able to decrease LC3-II expression and numbers of autophagosomes in mouse tissues and different cancer cell lines. Using bafilomycin A(1) treatment, we have observed that GADD45A regulates autophagosome initiation. Likely, GADD45A inhibition of autophagy is through its influence on the interaction between BECN1 and PIK3C3. Immunoprecipitation and GST affinity isolation assays exhibit that GADD45A directly interacts with BECN1, and in turn dissociates the BECN1-PIK3C3 complex. Furthermore, we have mapped the 71 to 81 amino acids of the GADD45A protein that are necessary for the GADD45A interaction with BECN1. Knockdown of BECN1 can abolish autophagy alterations induced by GADD45A. Taken together, these findings provide the novel evidence that GADD45A inhibits autophagy via impairing the BECN1-PIK3C3 complex formation.
分类: 生物学 >> 生物物理学 >> 生物力学与生物流变学 提交时间: 2016-05-15
摘要: B lymphocytes use B cell receptors (BCRs) to sense the physical features of the antigens. However, the sensitivity and threshold for the activation of BCRs resulting from the stimulation by mechanical forces are unknown. Here, we addressed this question using a double-stranded DNA-based tension gauge tether system serving as a predefined mechanical force gauge ranging from 12 to 56 pN. We observed that IgM-BCR activation is dependent on mechanical forces and exhibits a multi-threshold effect. In contrast, the activation of isotype-switched IgG- or IgE-BCR only requires a low threshold of less than 12 pN, providing an explanation for their rapid activation in response to antigen stimulation. Mechanistically, we found that the cytoplasmic tail of the IgG-BCR heavy chain is both required and sufficient to account for the low mechanical force threshold. These results defined the mechanical force sensitivity and threshold that are required to activate different isotyped BCRs.
分类: 生物学 >> 生物物理学 >> 生物物理、生物化学与分子生物学 提交时间: 2016-05-15
摘要: Genotoxic stress activates checkpoint signaling pathways that activate the checkpoint kinases ATM and ATR, halt cell cycle progression, and promote DNA repair. A number of proteins act in concert with ATR to phosphorylate Chk1, including RAD17, the RAD9-RAD1-HUS1 complex, ATR/ATRIP and TopBp1. However, how these proteins involved act in concert with one another to propagate and maintain the checkpoint response is not well understood. Here, we reported that upregulation of RAD9 protein increased the quantity of ATRIP, suggesting that RAD9 activation will induce more efficient accumulation of ATRIP in vivo. Furthermore, the DNA damage-induced ATRIP foci formation was faster in the mRad9(-/-) ES cells. Also, ATRIP interacts specifically with RAD9, but not HUS1 and RAD1. Taken together, we suggested that RAD9 could affect both the ATRIP protein levels and DNA damage-induced ATRIP foci formation. Thus, we propose a role of RAD9 in the ATR-Chk1 pathway that is necessary for successful formation of the damage-sensing complex and DNA damage checkpoint signaling.
分类: 生物学 >> 生物物理学 >> 生物物理、生物化学与分子生物学 提交时间: 2016-05-12
摘要: With the rapid development of high-throughput sequencing technologies, the emerging of methylated RNA immunoprecipitation sequencing (MeRIP-seq) technology makes it possible to detect RNA epigenetic modifications in a large scale, which allows transcriptome-wide profiling of RNA methylation. Mining the patterns of global mRNA methylation from these MeRIP-seq data can help reveal the potential functional roles of these mRNA methylations in regulating gene expression, splicing, RNA editing and RNA stability, effectively guiding the therapeutic intervention of cancer. Here, the principle of MeRIP-seq sequencing was first introduced. Then, the recent progress of the processing and analysis of MeRIP-seq data were comprehensively discussed. In the end, the computational problems and challenges faced in the process of MeRIP-seq data processing were also summarized.
分类: 生物学 >> 生物物理学 >> 生物物理、生物化学与分子生物学 提交时间: 2016-05-12
摘要: With the aim of broadening the versatility of lentiviral vectors as a tool in nucleic acid research, we expanded the genetic code in the propagation of lentiviral vectors for site-specific incorporation of chemical moieties with unique properties. Through systematic exploration of the structure-function relationship of lentiviral VSVg envelope by site-specific mutagenesis and incorporation of residues displaying azide- and diazirine-moieties, the modifiable sites on the vector surface were identified, with most at the PH domain that neither affects the expression of envelope protein nor propagation or infectivity of the progeny virus. Furthermore, via the incorporation of such chemical moieties, a variety of fluorescence probes, ligands, PEG and other functional molecules are conjugated, orthogonally and stoichiometrically, to the lentiviral vector. Using this methodology, a facile platform is established that is useful for tracking virus movement, targeting gene delivery and detecting virus-host interactions. This study may provide a new direction for rational design of lentiviral vectors, with significant impact on both basic research and therapeutic applications.
分类: 生物学 >> 生物物理学 >> 免疫学 提交时间: 2016-05-12
摘要: We previously showed that LIGHT and its receptor herpes virus entry mediator (HVEM) are important for development of optimal CD4(+) Th1 cell immunity and resistance to primary Leishmania major infection in mice. In this study, we further characterized the contributions of this molecule in dendritic cell (DC) maturation, initiation, and maintenance of primary immunity and secondary anti-Leishmania immunity. Flow-cytometric studies showed that CD8 alpha(+) DC subset was mostly affected by HVEM-Ig and lymphotoxin beta receptor-Ig treatment. LIGHT signaling is required at both the priming and the maintenance stages of primary anti-Leishmania immunity but is completely dispensable during secondary immunity in wild type mice. However, LIGHT blockade led to impaired IL-12 and IFN-gamma responses and loss of resistance in healed CD40-deficient mice after L. major challenge. The protective effect of LIGHT was mediated primarily via its interaction with lymphotoxin beta receptor on CD8 alpha(+) DCs. Collectively, our results show that although LIGHT is critical for maintenance of primary Th1 response, it is dispensable during secondary anti-Leishmania immunity in the presence of functional CD40 signaling as seen in wild type mice.