Understanding Fe2+ toxicity and P deficiency tolerance in rice for enhancing productivity under acidic soils

Plants experience low phosphorus (P) and high iron (Fe) levels in acidic lowland soils that lead to reduced crop productivity. A better understanding of the relationship between these two stresses at molecular and physiological level will lead to development of suitable strategies to increase crop productivity in such poor soils. Tolerance for most abiotic stresses including P deficiency and Fe toxicity is a quantitative trait in rice. Recent studies in the areas of physiology, genetics, and overall metabolic pathways in response to P deficiency of rice plants have improved our understanding of low P tolerance. Phosphorous uptake and P use efficiency are the two key traits for improving P deficiency tolerance. In the case of Fe toxicity tolerance, QTLs have been reported but the identity and role played by underlying genes is just emerging. Details pertaining to Fe deficiency tolerance in rice are well worked out including genes involved in Fe sensing and uptake. But, how rice copes with Fe toxicity is not clearly understood. This review focuses on the progress made in understanding these key environmental stresses. Finally, an opinion on the key genes which can be targeted for this stress is provided.     

Sitting above the maze: recent model discoveries in molecular science

The 2013 Nobel Prize in Chemistry has convinced the world that how important the role that computational sciences play in chemical and materials sciences. In this review, computational methods and rational molecule design, including quantum mechanics and molecular mechanics methods, have been applied to study electronic structures and the interactions in a number of important applications at molecular level. The applications which include bioactive compounds, drug candidates and photoactive molecules at Swinburne University in the past several years are discussed. The research is in close collaboration with world class experimental groups from spectroscopy, organic and medicinal synthesis laboratories and most recently to γ-ray spectroscopy as well as other theory groups in the world. Ionisation spectra of biomolecules and bioactive compounds including amino acids, DNA bases, cyclic dipeptides, drug candidates, complexes and photoactive molecules are discussed. Most recent projects such as infrared spectral studies of ferrocene, rational design of organic dyes in solar cell applications, and recent development in γ-ray spectra of positron annihilation in molecules are highlighted.     

生物耐铜的分子机理及铜污染环境的生物联合修复

铜是动植物和人类必需的微量元素,缺乏或过多都将产生不良影响。随着社会经济的发展,人类活动对环境的干扰日益加剧,工业和农业生产活动常可导致土壤铜污染,铜已成为土壤重金属污染的主要元素之一。总结了铜在植物体内的自发内稳态调节机制,在细菌和真菌体内的吸收、分布、解毒和调节因子,同时以蚯蚓为例简要阐述了土壤动物对铜的解毒机理;从分子生物学角度对重金属铜在生物体内的代谢机理及生物对环境中过量铜的联合修复研究进展进行了综述,以期为铜污染环境的植物、微生物和动物联合修复的分子机理研究提供借鉴。     

合成肽疫苗的分子设计

合成肽疫苗能克服常规疫苗的缺点,很早就被认为是动物传染病预防用的终极疫苗。然而多年的研究结果表明,合成肽疫苗免疫动物后所起的免疫保护作用并没有象人们当初设想的那样理想,同时证明了构建的合成肽疫苗的抗原性及其免疫原性要受到其自身组成及宿主免疫系统等多种因素的影响。在诱导机体产生免疫的过程中,单一的中和抗原表位是远远不够的,增加中和抗原表位的数目和引入细胞抗原表位将起到必不可少的辅助协同作用。若想提高合成肽疫苗的免疫效果,在搞清合成肽疫苗的免疫机理并在如何利用有限的抗原表位诱导强有力的免疫保护作用等方面需要做进一步深入地研究。     

Composition and lipid spatial distribution of HDL particles in subjects with low and high HDL-cholesterol

A low level of high density lipoprotein cholesterol (HDL-C) is a powerful risk factor for cardiovascular disease. However, despite the reported key role of apolipo-proteins, specifically, apoA-I, in HDL metabolism, lipid molecular composition of HDL particles in subjects with high and low HDL-C levels is currently unknown. Here lipidomics was used to study HDL derived from well-characterized high and low HDL-C subjects. Low HDL-C subjects had elevated triacylglycerols and diminished lysophosphatidylcholines and sphingomyelins. Using information about the lipid composition of HDL particles in these two groups, we reconstituted HDL particles in silico by performing large-scale molecular dynamics simulations. In addition to confirming the measured change in particle size, we found that the changes in lipid composition also induced specific spatial distributions of lipids within the HDL particles, including a higher amount of triacylglycerols at the surface of HDL particles in low HDL-C subjects. Our findings have important implications for understanding HDL metabolism and function. For the first time we demonstrate the power of combining molecular profiling of lipoproteins with dynamic modeling of lipoprotein structure.     

Molecular tools and bumble bees: revealing hidden details of ecology and evolution in a model system

Bumble bees are a longstanding model system for studies on behaviour, ecology and evolution, due to their well‐studied social lifestyle, invaluable role as wild and managed pollinators, and ubiquity and diversity across temperate ecosystems. Yet despite their importance, many aspects of bumble bee biology have remained enigmatic until the rise of the genetic and, more recently, genomic eras. Here, we review and synthesize new insights into the ecology, evolution and behaviour of bumble bees that have been gained using modern genetic and genomic techniques. Special emphasis is placed on four areas of bumble bee biology: the evolution of eusociality in this group, population‐level processes, large‐scale evolutionary relationships and patterns, and immunity and resistance to pesticides. We close with a prospective on the future of bumble bee genomics research, as this rapidly advancing field has the potential to further revolutionize our understanding of bumble bees, particularly in regard to adaptation and resilience. Worldwide, many bumble bee populations are in decline. As such, throughout the review, connections are drawn between new molecular insights into bumble bees and our understanding of the causal factors involved in their decline. Ongoing and potential applications to bumble bee management and conservation are also included to demonstrate how genetics‐ and genomics‐enabled research aids in the preservation of this threatened group.     

Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation

The hyperthermophilic Ssh10b from Sulfolobus shibatae is a member of the Sac10b family, which binds RNA in vivo as a physiological substrate, and it has been postulated to play a key role in chromosomal organization in Archaea. Even though the crystal structure of Ssh10b‐RNA was resolved successively by X‐ray diffraction (Protein Data Bank [PDB] code: 3WBM), the detailed dynamic characteristics of Ssh10b‐RNA are still unclear. In this study, molecular dynamics (MDs) simulations at 6 temperatures (300, 350, 375, 400, 450, and 500 K) and molecular mechanics Generalized‐Born surface area (MM‐GB/SA) free energy calculations were performed to investigate the mechanism of how Ssh10b protects and stabilizes RNA. The simulation results indicate that RNA is stabilized by Ssh10b when the temperature rises up to 375 K. RNA is found to undergo conformational transition between A‐RNA and A′‐RNA when Ssh10b binds to RNA at 3 different temperatures (300, 350, and 375 K). Salt bridges, hydrogen bonds and hydrophobic interactions are observed, and some residues have significant impact on the structural stability of the complex. This study increases our understanding of the dynamics and interaction mechanism of hyperthermophilic proteins and RNA at the atomic level, and offers a model for studying the structural biology of hyperthermophilic proteins and RNA.     

Single molecule fluorescence spectroscopy for quantitative biological applications

Single molecule techniques emerge as powerful and quantitative approaches for scientific investigations in last decades. Among them, single molecule fluorescence spectroscopy (SMFS) is able to non-invasively characterize and track samples at the molecular level. Here, applications of SMFS to fundamental biological questions have been briefly summarized in catalogues of single-molecule counting, distance measurements, force sensors, molecular tracking, and ultrafast dynamics. In these SMFS applications, statistics and physical laws are utilized to quantitatively analyze the behaviors of biomolecules in cellular signaling pathways and the mechanisms of biological functions. This not only deepens our understanding of bio-systems, but also provides a fresh angle to those fundamental questions, leading to a more quantitative thinking in life science.     

Multi-Scale Dimensions of Indigenous Land Tenure in the Amazon

This study demonstrates the importance of scale in understanding the common property institutions of indigenous groups in the Amazon. Using the example of the Pueblo Kichwa de Rukullakta, an ethnic Kichwa group in the Ecuadorian Amazon, we analyze land tenure arrangements at the household, community, and territory levels using a common property framework. The specific bundle of rights identified by the framework is held at the household level but households rely on community and territory level arrangements for their enforcement. Land claims at the community and territory level also serve to define the pool of legitimate rights holders at the next lower level. Due to the importance of scale in understanding indigenous land tenure generally, we suggest an adaptation of the common property framework to explicitly recognize the role of scale. This adapted framework identifies the function, characteristics, and means of enforcement for land claims at each scale of analysis.     

稻田穗期主要捕食性天敌对两种盲蝽集团内捕食的初步研究

【目的】集团内捕食是影响农业系统广食性天敌对靶标害虫控制作用的重要因素,全面揭示稻田广食性天敌对稻飞虱重要天敌黑肩绿盲蝽Cyrtorhinus lividipennis Reuter和中华淡翅盲蝽Tytthus chinensis(St?l)(半翅目:盲蝽科)的集团内捕食作用有助于更好地保护利用天敌。【方法】建立以两种盲蝽为猎物对象的种特异性二重定量PCR系统,检测比较不同抗性品种穗期田间主要捕食者对两种盲蝽的集团内捕食作用。【结果】(1)本研究建立的二重定量PCR具有的物种专化性,两种检测靶标灵敏度高且相似,可用于田间捕食者猎物分析;(2)感虫水稻品种上捕食者对盲蝽的捕食强度高于抗性水稻品种;不同种类捕食者对盲蝽的集团内捕食强度有显著差异;捕食者对黑肩绿盲蝽集团内捕食强度显著高于中华淡翅盲蝽。【结论】捕食性盲蝽在稻田生态系统遭遇集团内捕食,其集团内捕食强度与水稻品种抗性、捕食者种类和猎物丰富度有关。     

Advances in higher-order chromatin architecture: the move towards 4D genome

In eukaryotes, the genome is hierarchically packed inside the nucleus, which facilitates physical contact between cis-regulatory elements (CREs), such as enhancers and promoters. Accumulating evidence highlights the critical role of higher-order chromatin structure in precise regulation of spatiotemporal gene expression under diverse biological contexts including lineage commitment and cell activation by external stimulus. Genomics and imaging-based technologies, such as Hi-C and DNA fluorescence in situ hybridization (FISH), have revealed the key principles of genome folding, while newly developed tools focus on improvement in resolution, throughput and modality at single-cell and population levels, and challenge the knowledge obtained through conventional approaches. In this review, we discuss recent advances in our understanding of principles of higher-order chromosome conformation and technologies to investigate 4D chromatin interactions.     

Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin

Thrombin is an attractive target for antithrombotic therapy due to its central role in thrombosis and hemostasis as well as its role in inducing tumor growth, metastasis, and tumor invasion. The thrombin-binding DNA aptamer (TBA), is under investigation for anticoagulant drugs. Although aptamer binding experiments have been revealed various effects on thrombin’s enzymatic activities, the detailed picture of the thrombin’s allostery from TBA binding is still unclear. To investigate thrombin’s response to the aptamer-binding at the molecular level, we compare the mechanical properties and free energy landscapes of the free and aptamer-bound thrombin using microsecond-scale all-atom GPU-based molecular dynamics simulations. Our calculations on residue fluctuations and coupling illustrate the allosteric effects of aptamer-binding at the atomic level, highlighting the exosite II, 60s, γ and the sodium loops, and the alpha helix region in the light chains involved in the allosteric changes. This level of details clarifies the mechanisms of previous experimentally demonstrated phenomena, and provides a prediction of the reduced autolysis rate after aptamer-binding. The shifts in thrombin’s ensemble of conformations and free energy surfaces after aptamer-binding demonstrate that the presence of bound-aptamer restricts the conformational freedom of thrombin suggesting that conformational selection, i.e. generalized allostery, is the dominant mechanism of thrombin-aptamer binding. The profound perturbation on thrombin’s mechanical and thermodynamic properties due to the aptamer-binding, which was revealed comprehensively as a generalized allostery in this work, may be exploited in further drug discovery and development.     

Understanding the physical basis of memory: Molecular mechanisms of the engram

Memory, defined as the storage and use of learned information in the brain, is necessary to modulate behavior and critical for animals to adapt to their environments and survive. Despite being a cornerstone of brain function, questions surrounding the molecular and cellular mechanisms of how information is encoded, stored, and recalled remain largely unanswered. One widely held theory is that an engram is formed by a group of neurons that are active during learning, which undergoes biochemical and physical changes to store information in a stable state, and that are later reactivated during recall of the memory. In the past decade, the development of engram labeling methodologies has proven useful to investigate the biology of memory at the molecular and cellular levels. Engram technology allows the study of individual memories associated with particular experiences and their evolution over time, with enough experimental resolution to discriminate between different memory processes: learning (encoding), consolidation (the passage from short-term to long-term memories), and storage (the maintenance of memory in the brain). Here, we review the current understanding of memory formation at a molecular and cellular level by focusing on insights provided using engram technology.     

Functional Differentiation of Multiple Dopamine D1-Like Receptors by NNC 01-0012

Abstract: Although members of the multiple vertebrate/mammalian dopamine D1 receptor gene family can be selectively classified on the basis of their molecular/phylogenetic, structural, and tissue distribution profiles, no subtype-specific discriminating agents have yet been identified that can functionally differentiate these receptors. To define distinct pharmacological/functional attributes of multiple D1-like receptors, we analyzed the ligand binding profiles, affinity, and functional activity of 12 novel NNC compounds at mammalian/vertebrate D1/D1A and D5/D1B, as well as vertebrate D1C/D1D, dopamine receptors transiently expressed in COS-7 cells. Of all the compounds tested, only NNC 01-0012 displayed preferential selectivity for vertebrate D1C receptors, inhibiting [³H]SCH-23390 binding with an estimated affinity (∼0.6 n M ) 20-fold higher than either mammalian/vertebrate D1/D1A or D5/D1B receptors or the D1D receptor. Functionally, NNC 01-0012 is a potent antagonist at D1C receptors, inhibiting to basal levels dopamine (10 µ M )-stimulated adenylyl cyclase activity. In contrast, NNC 01-0012 (10 µ M ) exhibits weak antagonist activity at D1A receptors, inhibiting only 60% of maximal cyclic AMP production by dopamine, while acting as a partial agonist at vertebrate D1B and D1D receptors, stimulating adenylyl cyclase activity by ∼33% relative to the full agonist dopamine (10 µ M ), an effect that was blocked by the selective D1 receptor antagonist NNC 22-0010. These data clearly suggest that the benzazepine NNC 01-0012, despite lacking the N -methyl residue in the R3 position, is a selective and potent D1C receptor antagonist. Moreover, the differential signal transduction properties exhibited by NNC 01-0012 at these receptor subtypes provide further evidence, at least in vertebrates, for the classification of the D1C receptor as a distinct D1 receptor subtype.     

Atomistic MD simulation reveals the mechanism by which CETP penetrates into HDL enabling lipid transfer from HDL to CETP

Inhibition of cholesterol ester transfer protein (CETP), a protein mediating transfer of neutral lipids between lipoproteins, has been proposed as a means to elevate atheroprotective HDL subpopulations and thereby reduce atherosclerosis. However, off-target and adverse effects of the inhibition have raised doubts about the molecular mechanism of CETP-HDL interaction. Recent experimental findings have demonstrated the penetration of CETP into HDL. However, atomic level resolution of CETP penetration into HDL, a prerequisite for a better understanding of CETP functionality and HDL atheroprotection, is missing. We constructed an HDL particle that mimics the actual human HDL mass composition and investigated for the first time, by large-scale atomistic molecular dynamics, the interaction of an upright CETP with a human HDL-mimicking model. The results demonstrated how CETP can penetrate the HDL particle surface, with the formation of an opening in the N barrel domain end of CETP, put in evidence the major anchoring role of a tryptophan-rich region of this domain, and unveiled the presence of a phenylalanine barrier controlling further access of HDL-derived lipids to the tunnel of CETP. The findings reveal novel atomistic details of the CETP-HDL interaction mechanism and can provide new insight into therapeutic strategies.     

Pathways and intermediates of amyloid fibril formation

The lack of understanding of amyloid fibril formation at the molecular level is a major obstacle in devising strategies to interfere with the pathologies linked to peptide or protein aggregation. In particular, little is known on the role of intermediates and fibril elongation pathways as well as their dependence on the intrinsic tendency of a polypeptide chain to self-assembly by β-sheet formation (β-aggregation propensity). Here, coarse-grained simulations of an amphipathic polypeptide show that a decrease in the β-aggregation propensity results in a larger heterogeneity of elongation pathways, despite the essentially identical structure of the final fibril. Protofibrillar intermediates that are thinner, shorter and less structured than the final fibril accumulate along some of these pathways. Moreover, the templated formation of an additional protofilament on the lateral surface of a protofibril is sometimes observed as a collective transition. Conversely, for a polypeptide model with a high β-aggregation propensity, elongation proceeds without protofibrillar intermediates. Therefore, changes in intrinsic β-aggregation propensity modulate the relative accessibility of parallel routes of aggregation.