Comparison of the Biological Activity and Constituents in Japanese Ambers

Background/Aim: Kuji amber is an interesting natural source for drug discovery because a new anti-allergic compound, named kujigamberol and several new compounds have been isolatated from it. It was important to evaluate the yield, biological activities and constituents of each methanol extract of Kuji, Iwaki, Choshi, Mizunami and Ube ambers in Japan in order to establish if additional new compounds could be identified in these ambers. Materials and Method: Biological activities of each extract were evaluated using growth-restoring activity of the mutant yeast strain involving Ca2+-signal transduction and inhibition activity of degranulation in rat basophilic leukemia (RBL)-2H3 cells. Constituents of each extract were analyzed by high performance liquid chromatography (HPLC). Results: All ambers except Ube amber have growth-restoring activity against the mutant yeast. Both Kuji and Iwaki ambers inhibited the degranulation of RBL-2H3 cells induced by the calcium ionophore A23187 in a dose dependent manner. The main biologically active compound in Kuji amber, kujigamberol, was also isolated from Iwaki amber and analyzed by mass spectrometry (MS) and nuclear magnetic resonance (NMR). Conclusion: Kuji and Iwaki ambers appeared to have the same origin. Choshi, Mizunami, and Ube ambers are valuable sources for biologically active compounds which are different from those of Kuji amber.

Fern Diversity in the Mid-Cretaceous Amber Forests Revealed by Exceptionally Preserved Sporangium Types

The amber deposits from the Albian-Cenomanian in Myanmar have emerged as a pivotal source for exceptionally abundant fossil insect fauna since their initial discovery. Recent studies have increasingly focused on elucidating the fern inventory and examining newly available fossils from Myanmar amber, suggesting a diverse fern flora that once thrived in Cretaceous forests. Through investigations of amber collections, with particular emphasis on sporangium structures—especially the annulus types preserved in amber inclusions—this study revealed additional novelties within the Cyatheales and Schizaeales in mid-Cretaceous Myanmar amber forests. The described specimens and newly discovered fossils provide compelling evidence that Polypodiales were not only diverse and abundant but also that other fern lineages, such as Cyatheales and Schizaeales, coexisted in these ancient forest ecosystems. This study reveals the high diversity of ferns in the mid-Cretaceous Myanmar area, while also implying the paleoecological and paleogeographical significance of the Mesozoic Burmese amber forests.

Succinite, Baltic Amber:A Chemical Masterpiece of Nature

Succinite,Baltic amber,is one of the most appreciated fossil resins.Its beauty has fascinated people since prehistoric times.It is a substance,and also gemstone,whose uniqueness is due to its compelling,though still not fully understood,physicochemical nature.In this article,some facts about the physical and chemical properties of succinite in order to find an answer for questions about the unique properties of this resin,such as color,transparency,texture etc.,are discussed.These properties are among the factors that determine the choice of Baltic amber as a gemstone.Commonly known properties of succinite,but also some less obvious features,have been linked to the organic and inorganic chemical composition and structural factors,including the sophisticated supramolecular structure masterfully created by nature.Changes of the properties of succinite used as a jewelry stone are discussed as a reflection of changes in its physicochemical nature.In this light,some methods that can be used to identify succinite(i.e.,infrared spectroscopy and nuclear magnetic resonance spectroscopy)and their relevance to the classification of fossil resins are briefly discussed.This article highlights an important point:only by understanding the chemical and physical nature of the material we able to identify,modify and effectively use the goods that have been given to us by mother nature.

Room-Temperature Phosphorescence and Lifetime of Fossil Resins (Amber) from Dominican Republic, Mexico, Baltic Sea, Myanmar, and Fushun, China

Amber can emit room temperature phosphorescence(RTP)under the well-known 365 nm fluorescence ultraviolet light.This paper is devoted to the phosphorescence study of 20 pieces of amber materials from the Dominican Republic,Mexico,Baltic sea,Myanmar,and Fushun,China.The results show that amber from the same geographic origin has similar shape in phosphorescence spectra.However,the shape of the amber phosphorescence spectra varies depending on their different localities.Burmite(amber from Myanmar)and Fushun amber have a bright yellow phosphorescence with a long lifetime,while the Dominican and Mexican ones are weaker and last shorter.The irradiation of Baltic amber becomes faint or even inert.Phosphorescence spectral Gaussian fitting results suggest an emission maximum near 550 nm in most amber samples.Their phosphorescence lifetime,analyzed through the exponential function fitting,is up to 1 second in Burmite and Fushun samples,shorter in the Dominican and Mexican ones,about 0.230 s,and the shortest in Baltic amber,close to 0.151 s.These variations of phosphorescence lifetime and intensity are related to the relative geological ages of these amber.It indicated that the phosphorescence agent was probably formed during the long geological time.While the anomaly occurred in Baltic amber,the only one found in a sea secondary deposit form,it demonstrated that the terrestrial geological environment these amber preserved has prevented the phosphorescence agent to be deactivated.

Ant Pupae from Myanmar Amber Reveal the Evolutionary Process of Cocoon-Spinning Behavior in Formicidae

Many extant species spin cocoons before their pupal stage,which can protect them from predators,pathogens,and fluctuant environmental factors in nests.However,owing to the scarcity of ant cocoon fossils,little is known about the origin and evolution of this behavior in Formicidae.Here,we describe two ant pupae specimens from Myanmar amber.The presence of cocoons in these Mesozoic fossils suggests the ancestral origin of spinning cocoon behavior;based on our phylogenetic analysis and ancestral state reconstruction,this behavior was secondarily lost at least six times in Formicidae,which could be ascribed to the transition of nesting and feeding habits,as well as the development of eusociality.Moreover,the first specimen preserved worker ants with empty cocoons simultaneously,indicating garbage removal or brood care behavior,which improves our understanding of their eusociality in the Cretaceous.

一组和AMBER力场配合的普适波恩模型参数

提出了一套和AMBER力场相匹配的普适波恩模型参数.新的参数集包含21种原子类型的初始半径和屏蔽因子.参数通过遗传算法拟合359个小分子水合自由能的实验值得到.采用新的参数,预测了44个小分子的水合自由能,预测值和实验值能很好地吻合,而且大大优于采用Jayaram参数得到的结果.此外,采用新的参数,还预测了15个蛋白质的水合自由能,预测值和PB/SA预测得到的结果能很好地吻合.

栗钙土胡敏酸分子三维结构模型构建及其优化

本研究的目的在于确定胡敏酸的分子结构,探究其结构与性质的关系。综合应用了元素分析、红外光谱、13C核磁共振波谱等仪器分析方法对内蒙古草原样地栗钙土土壤的胡敏酸分子结构特征进行比较分析,并基于实验结构数据构建了土壤胡敏酸结构单元模型,通过模拟光谱与实际光谱比较验证了构建的二维结构有很大的可适性。借助Hyperchem软件,在MM+、AMBER、OPLS三种力场下应用分子模拟方法对三维单体结构进行分子力学、分子动力学结构优化。结果表明土壤胡敏酸的三维结构单体在AMBER力场下生成热最小,等于-1638.87 kJ/mol,所以其构象最为稳定。同时模拟其处于水环境下的分子结构,总势能及各种能量在优化前后有变化,但总体来说各种状态都较稳定。

AMBER软件介绍

介绍了用于放射性废物处置系统安全评价的AMBER软件的应用范围、特点、使用限制和步骤,及其所包含的几个应用实例。

图形软件与Amber程序的联合应用

根据分子动力学模拟软件Amber的使用流程,分析了几种图形软件在相应流程中的应用.分子动力学模拟与图形软件的有机结合,大大简化了对所模拟的分子特别是生物大分子的分析,使输入和输出文件都变得更加方便直观.

多核CPU和GPU加速分子动力学模拟

在多核中央处理器(CPU)—图形处理器(GPU)异构并行体系结构上,采用OpenMP和计算统一设备架构(CUDA)编程实现了基于AMBER力场的蛋白质分子动力学模拟程序。通过合理地将程序划分为CPU单线程、CPU多线程和GPU多线程执行部分,高效地利用了计算机的处理能力。性能测试结果表明,相对于优化后的CPU串行计算,多核CPU-GPU异构并行计算模型有强大的性能优势,特别是将占整个程序执行时间90%的作用力的计算移植到GPU上执行,获得了最高可达12倍的计算加速比。

HIV-1蛋白酶异位抑制剂体系的长时间分子动力学模拟

采用新开发的ff12SB力场在NVIDIA CUDA GPU上对HIV-1蛋白酶的活性位抑制剂体系和异位抑制剂体系分别进行了100 ns的长时间分子动力学模拟,并用MM-PB/GBSA方法计算了活性位点抑制剂TL-3与HIV-1蛋白酶的结合自由能。异位抑制剂体系中分子片段2-甲基环己醇结合在Exo位,有利于抑制剂被束缚在活性位点附近。异位抑制剂体系中抑制剂TL-3与蛋白酶的结合自由能为-85.78 kcal/mol,活性位抑制剂体系中为-79.45 kcal/mol。这些结果有助于深入了解HIV-1 PR的动力学过程,为设计新型强效抑制剂提供了新见解。

鼠伤寒沙门氏菌嘌呤生物合成的调控研究X.purR琥珀突变体(am)的分离和氨基酸取代的初步研究

以超阻遏突变体３—１８为出发株，采用以乳糖为唯一碳源的ＮＣＥ平板的方法分离到４３９ 株调节突变体。通过转导引入ｔＲＮＡ抑制基因从中检测到 １１株 ｐｕｒＲ（ａｍ）候选株。共转导分 析证明，这些突变株的琥珀浪突变均发生在ｐｕｒＲ上。用 ｓｕｐＤ． ｓｕｐＥ和 ｓｕｐＦ分别对上述各ａｍｂｅｒ 突变体作了氨基酸取代实验，初步结果表明：同一氨基酸对ｐｕｒＲ不同位点（ａｍ）的氨基酸取 代，对ＰｕｒＲ调节功能有不同程度的影响。不同氨基酸（３种）对ｐｕｒＲ同一位点（ａｍ）的氨基酸取 代，对其调节功能的影响也存在差异。

不同力场对B-DNA到A-DNA构型转变的影响

采用分子动力学模拟方法比较了最新版CHARMM和AMBER(包括bsc1和OL15)力场对水溶液中B-DNA到A-DNA转化过程的影响,利用扩展自适应偏置力(eABF)方法计算了转化过程的自由能变化.研究结果表明,在不同力场下,水环境中的DNA最稳定结构存在差异,AMBER力场比CHARMM力场更符合实验结果.AMBER力场下DNA最稳定结构的小沟较窄,稳定于B构型;而CHARMM力场下DNA最稳定结构的小沟较宽,介于B构型与A构型之间.通过分析DNA周围离子及水的分布情况发现,CHARMM力场下DNA小沟周围的离子密度明显低于AMBER力场,不能很好地抵消2条磷酸骨架之间的排斥作用,这是CHARMM力场下小沟较宽且趋向A构型的主要原因.

天然橡胶热解行为的分子动力学模拟研究

为了了解天然橡胶热解过程及其热解产物,本文基于AMBER力场,对聚合度为10的橡胶模型的热解过程进行分子动力学模拟。建立周期性边界条件,分子力场采用谐振子模型计算键角弯曲能和键伸缩能,并通过Hyperchem软件进行热解模拟。模拟结果表明,在低温加热过程中,原子内部结构发生了一些物理变化,原子之间的键长变大,键角变得弯曲,原子间二面角增大,但由于范德华力与静电的限制,没有出现化学键的断裂;当温度达到600K左右时,分子键会发生断裂,形成各种大分子碎片,产物主要以液态油形式存在,粘性大,随着温度进一步升高,大分子碎片会分解成小分子碎片,气体产物增加,粘性变小。由此说明,温度对橡胶产物的影响较大,不同的温度下所获得的产物不同,因此,可以通过控制温度来获得所需的物质。该研究对于回收利用废橡胶具有重要意义。

MDM2蛋白与抑制剂IMZ相互作用的研究

癌症是最难攻克的疾病之一,它被认为是基因疾病[1].P53是一种癌抑制蛋白,而MDM2是一种绑定在P53上致使其失去活性的一种癌蛋白,P53失去活性意味着癌症的发生.本文论述的是抑制剂IMZ(药物)与MDM2蛋白的相互作用,作用的目的是打断MDM2与P53的结合,使P53保持活性,这样就可以用来抑制癌症[2].

Palynological Analysis of Amber-Bearing Clay from the Lower Cretaceous of Central Lebanon

An amber-bearing lignitic layer of sandy clay from the Lower Cretaceous of Central Lebanon （Mderej-Hammana）yielded a well-preserved,moderately variegated palynoflora,which origin is mixed between land plants and marine microflora.Its detailed analysis led to fulfill its inventory,to propose a paleoenvironmental reconstruction,and to draw the paleoclimate which prevailed over the region：an estuarian area under a rather humid,temperate climate;a variety of ferns grew near the shore-side and in the inward land.A tiny piece of amber containing angiospermous pollen grains of stratigraphical interest allows a precise dating.The marine microflora,poorly diversified,includes chitinous foraminifer linings and dinoflagellate cysts,among which Early Aptian guide taxa are present;their occurrence slightly narrows the stratigraphical range indicated by some palynological taxa which are related to land plants.

镎(Ⅳ)、镅(Ⅲ)、锔(Ⅲ)的AMBER力场参数化及评估

锕系元素具有高放射性和毒性,为开展锕系水溶液化学的实验研究带来了困难与挑战。得益于理论计算方法和计算能力的快速发展,运用分子动力学模拟水溶液环境并研究锕系在水溶液当中的化学行为成为一种可替代的方法。本文拟合了Np^4+、Am^3+、Cm^3+三种金属离子的力场参数并进行了评估,进而将其用于溶液配位化学和动力学研究。为了研究的系统性,也开展了Th^4+、U^4+、Pu^4+三种锕系离子的分子模拟研究。基于对上述六种离子的分子动力学研究,系统报道了该六种锕系离子的第一、二溶剂化层结构、性质、立体化学及驻留时间等方面的共性与特性,并从能量方面探究这些内在差异的原因。结果显示,本文报道的参数适用于锕系离子的配位结构和结合自由能的研究,但对于动力学性质的研究,宜谨慎用于相同价态的锕系离子溶液体系的定性理解。本文也探究了六种锕系离子在水溶液中与Cl^-、NO_3^-和CO_3^(2-)的相互作用,分析了各配合物配位模式、成键规律及结合强弱。综上所述,本项工作发展了三种关键锕系离子的力场参数,有助于开展基于AMBER力场的动力学方法的An^3+/^4+溶液化学的研究,丰富了对An^3+/^4+的水溶液中配位化学的认识。

First Psocodean (Psocodea,Empheriidae) from the Cretaceous Amber of New Jersey

Representatives of the extinct psocid family Empheriidae are known from Eocene Baltic amber, Lowermost Eocene French amber （Oise）, and Lower Cretaceous Spanish amber （Alava）. We report herein the first discovery of an empheriid psocid from the Cretaceous amber of New Jersey as Jerseyempheria grimaldii gen. et sp. nov. The fossil is figured and described. The new species is distinguished from related taxa. A discussion and checklist of Empheriidae are provided.

A New Species Group in the Genus Tanytarsus van der Wulp (Diptera:Chironomidae) Based on a Fossil Record from Baltic Amber

A new fossil chironomid, Tanytarsus serafini, found in Baltic amber is described and illustrated based on adult males. The new species and similar extant species of the genus Tanytarsus van der Wulp are compared. Due to several distinct characters of wing, legs and bypopygium, a new species group for Tanytarsus serafini is proposed, and its diagnostic features are evaluated.

Mesozoic Evaniidae (Insecta:Hymenoptera) in Spanish Amber:Reanalysis of the Phylogeny of the Evanioidea

One new genus and five new species of the family Evaniidae are described from the Early Cretaceous （Albian） Spanish amber of Pefiacerrada-I （Province of Burgos）, San Just and Arroyo de la Pascueta （both in the Province of Teruel）： Cretevania alonsoi sp. nov., C. montoyai sp. nov., C. alcalai sp. nov., C. rubusensis sp. nov., and lberoevania roblesi gen. and sp. nov. Taxonomic changes include Cretevania pristina （Zhang and Zhang, 2000） comb. nov., C. exquisita （Zhang, Rasnitsyn, Wang and Zhang, 2007） comb. nov., C. vesca （Zhang, Rasnltsyn, Wang and Zhang, 2007） comb. nov., and C. cyrtocerca （Deans, 2004） comb. nov., as a result of the reinterpretation of the genera Procretevania and Eovernevania. The new well preserved specimens of the genus Cretevania, together with the characters shown by the type specimens of the synonymized genera, give new information about their anatomical characters of taxonomical importance, and the genus Cretevania Rasnitsyn, 1975 is re-diagnosed. The holotypes of the Russian species in amber have been revised. A cladistic analysis of fossil and extant groups of the superfamily Evanioidea is included. Cretevania had a wide palaeogeographic distribution, with the highest diversity known from Spain. The 13 known Cretevania species show a high interspecific variation mainly in wing characteristics, and a wide range of body and wing size.