A comparison of four different conformations adopted by human telomeric G‐quadruplex using computer simulations

The telomeric G‐quadruplexes for their unique structural features are considered as potential anticancer drug targets. These, however, exhibit structural polymorphism as different topology types for the intra‐molecular G‐quadruplexes from human telomeric G‐rich sequences have been reported based on NMR spectroscopy and X‐ray crystallography. These techniques provide detailed atomic‐level information about the molecule but relative conformational stability of the different topologies remains unsolved. Therefore, to understand the conformational preference, we have carried out quantum chemical calculations on G‐quartets; used all‐atom molecular dynamics (MD) simulations and steered molecular dynamics (SMD) simulations to characterize the four human telomeric G‐quadruplex topologies based on its G‐tetrad core‐types, viz., parallel, anti‐parallel, mixed‐(3 + 1)‐form1 and mixed‐(3 + 1)‐form2. We have also studied a non‐telomeric sequence along with these telomeric forms giving a comparison between the two G‐rich forms. The structural properties such as base pairing, stacking geometry and backbone conformations have been analyzed. The quantum calculations indicate that presence of a sodium ion inside the G‐tetrad plane or two potassium ions on both sides of the plane give it an overall planarity which is much needed for good stacking to form a helix. MD simulations indicate that capping of the G‐tetrad core by the TTA loops keep the terminal guanine bases away from water. The SMD simulations along with equilibrium MD studies indicate that the parallel and non‐telomeric forms are comparatively less stable. We could come to the conclusion that the anti‐parallel form and also the mixed‐(3 + 1)‐form1 topology are most likely to represent the major conformation., 2016. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 83–99, 2016     

乳酸链球菌素对瘤胃体外发酵、甲烷生成及功能菌群数量的影响北大核心CSCD

【目的】旨在通过体外静态模拟瘤胃发酵法研究乳酸链球菌素(NI)对瘤胃发酵、甲烷生成及功能菌群数量的影响。【方法】以不添加任何添加剂处理做阴性对照(NC),以莫能菌素(MON,5μmol/L)做阳性对照,试验组NI添加水平分别为3(NI-3)、9(NI-9)和27 mg/100 m L(NI-27),每个处理4个重复,分别于培养后的0、3、6、9、12、24 h测定产气量和甲烷产量。培养24 h后,采集发酵液样品,用于发酵参数和菌群数量的测定。【结果】与NC组相比,添加NI和MON均能显著降低产气量和甲烷产量(P<0.05);添加NI对pH值、干物质消失率(DMD)和有机物消失率(OMD)无显著影响(P>0.05);NI-9处理组与NC组相比氨态氮浓度显著降低(P<0.05),而NI-3和NI-27组氨氮浓度没有显著变化(P>0.05);相比而言,MON处理组DMD、OMD和氨氮浓度与NC组相比均显著降低(P<0.05),而pH值与其他各处理组相比没有差异(P>0.05);与NC组相比,NI各处理组和MON组乙酸浓度及乙丙比均显著降低(P<0.05),丙酸浓度显著提高(P<0.05)。功能菌方面,qPCR结果显示添加NI和MON对总菌和拟杆菌门数量均无显著影响(P>0.05);与NC相比,添加NI对原虫、甲烷菌、真菌和厚壁菌门数量均无显著影响(P>0.05),而MON组原虫、甲烷菌、真菌和厚壁菌门数量显著降低(P<0.05);NI和MON处理均显著提高了硫还原菌和C.aminophilum数量(P<0.05),但C.sticklandii数量不受影响(P>0.05)。【结论】添加适宜浓度的NI可降低瘤胃甲烷与氨的生成,但并不影响饲料消化,这种发酵模式的改变可能与瘤胃功能菌群数量与多样性的变化密切相关。     

Effect of surface-screening parameter of the Yukawa potential model on vapour–liquid phase coexistence and critical-point properties of confined Yukawa fluid

We report the effect of surface-screening parameter of Yukawa potential model on vapour–liquid phase coexistence and critical-point properties of slit–pore-confined Yukawa fluid, using grand canonical transition-matrix Monte Carlo along with the histogram reweighting method. The effect of surface-screening parameter on the vapour–phase coexistence density is insignificant for the studied system. On the other hand, significant effect of surface-screening parameter is observed on liquid phase coexistence density. With increasing surface-screening parameter, liquid phase coexistence density decreases. Critical-point properties have shown monotonic decreasing trends with increase in surface-screening parameter. Moreover, the effect of change of surface-screening parameter is least on critical temperature changes as compared to critical density and critical pressure changes for the studied Yukawa system in this work.     

Probing the effect of nitro groups in nitramine based energetic molecules: a DFT and charge density study

The structure, electron density distribution, energetic and electrostatic properties of simple nitramine based energetic TMA, DMNA, MDA and TNA molecules were determined using density functional theory (B3LYP) with the 6-311G^** and aug-cc-pVDZ basis sets coupled with Bader's theory of atoms in molecules. In the NO₂ group substituted molecules, the N–N bond distance increases with the increase of NO₂ groups, whereas in C–N bonds, this effect is relatively less, and the distances are almost equal. The topological analysis of electron density reveals that the electron density ρ_bcp(r) of C–N and N–N bonds are significantly decreasing with the increase of NO₂ groups in the nitramine molecules. The Laplacian of electron density ▽²ρ_bcp(r) of N–NO₂ bonds [DMNA: ? 16.7 eÅ^? 5, MDA: ? 12.8 eÅ^? 5 and TNA: ? 7.9 eÅ^? 5] of the molecules are relatively less negative, and the values also decrease with the increase of NO₂ groups; this implies that the charge concentration decreases with the increase of NO₂ groups, which leads to weakening the N–N bonds of the molecules. The isosurface of molecular electrostatic potential displays high electronegative regions around the NO₂ groups. The oxygen balance OB₁₀₀ of the molecules increases as the number of NO₂ group increases in the molecules, in which, the TNA molecule having maximum OB₁₀₀ value [+7.89]. The band gap, heat of detonation, bond dissociation energy and charge imbalance are predominantly depends on the number of NO₂ group present in the molecule. The charge imbalance parameter (ν) has been calculated for all molecules, which reveals that TNA is a highly sensitive molecule, the corresponding ν value is 0.047.     

皮下种植黑色素瘤对小鼠血液中脂肪和氨基酸代谢的影响*

目的:探讨皮下种植黑色素瘤对小鼠血液中相关脂肪和氨基酸代谢的影响。方法:野生型小鼠皮下种植B16黑色素瘤细胞,两周后观察小鼠并取不同的组织称重,检测血液中甘油三酯、葡萄糖、脂肪酸、炎症因子的水平。利用质谱方法检测血液中氨基酸的水平。结果:野生型小鼠皮下肿瘤种植2周后体重没有明显变化,脾脏和肝脏的重量明显增加,皮下脂肪组织和腹腔脂肪组织的重量没有明显变化。血液中甘油三酯的水平明显增高,葡萄糖和甘油的水平明显下降。血液中炎症因子Interleukin 6(IL6)和Interferon gamma(IFNγ)的水平明显增加。血液的质谱结果显示有四种氨基酸的水平有明显变化,其中胱氨酸(Cystine)增加了约30倍,丝氨酸(Serine)、谷氨酰胺(Glutamine)和色氨酸(Tryptophan)分别有不同程度的降低。结论:皮下黑色素瘤显著影响小鼠机体营养状态和炎症,并特异性影响血液中氨基酸的代谢。     

米槁幼苗光合作用及光响应曲线模拟对干旱胁迫的响应

为阐明米槁光合作用对干旱胁迫的响应规律与适应机制,以一年生米槁幼苗为研究对象,进行盆栽试验研究设置3种不同土壤含水量梯度,利用Li-6400便携式光合作用系统测定干旱胁迫下的光合生理指标及光响应过程,光响应曲线模拟采用直角双曲线模型、非直角双曲线模型、指数模型和直角双曲线修正模型进行拟合并对比,以期选出适用于干旱环境下的光响应模型。结果表明(1)光响应曲线模型对干旱胁迫下米槁幼苗的光合作用拟合中直角双曲线、非直角双曲线和指数模型适用于低光合有效辐射(PAR),但拟合光响应参数与实测值相差大,只有直角双曲线修正模型能够很好的拟合各个处理且拟合参数比较精确米槁幼苗。(2)光合作用的表观量子效率(Φ)小于一般植物的光合量子效率,则其对弱光的光能利用效率相对较低。(3)在较强的光合有效辐射条件下,严重干旱胁迫下的米槁净光合速率P_n显著下降,出现了明显的光抑制现象;中度胁迫下净光合速率(P_n)、最大净光合速率(P_(nmax))、光补偿点(LSP)最大,米槁具有较宽的抗旱适应范围,有一定的抗旱性;严重胁迫下P_n、P_(nmax)、LSP降低,蒸腾速率(T_r)与气孔导度(G_s)下降幅度更大,但仍具有较高的水分利用效率(WUE),米槁在严重的干旱胁迫下光合机构受到一定的损伤,但自身可以通过生理调节来积极适应不良环境,减少光合机构伤害。(4)综合来看,在人工管理或种植米槁时,为了适应米槁生长发育,建议土壤含水量保持在23.05%到14.92%之间。     

镧胁迫下外源H2O2对裸燕麦幼苗叶绿素荧光参数和光合碳同化酶活性的影响

稀土污染已成为制约农业发展的一种重要因素,为探讨外源过氧化氢(H_2O_2)缓解裸燕麦镧(La)胁迫伤害的光合生理机制,以‘白燕7号’裸燕麦幼苗为材料,采用砂培方法,研究了5 mmol/L H_2O_2喷施预处理对1.20 mmol/L La~(3+)胁迫下裸燕麦幼苗生长、叶片叶绿素荧光参数和碳同化关键酶活性的影响。结果表明:La胁迫下,H_2O_2预处理的裸燕麦幼苗根长、株高和生长量的降幅及叶片叶黄素循环脱环氧化状态(A+Z)/(V+A+Z)显著下降,PSⅡ最大光化学效率(F_v/F_m)、实际光化学效率(Φ_(PSⅡ))、光化学猝灭系数(qP)和吸收光能用于光化学反应的份额(P)显著提高,PSⅡ非光化学猝灭系数(NPQ)、调节性能量耗散Y(NPQ)、非调节性能量耗散Y(NO)、吸收光能用于天线热耗散的份额(D)、PSⅡ反应中心非光化学耗散的份额(E_x)和双光系统间激发能分配不平衡偏离系数(β/α-1)明显降低,同时1, 5-二磷酸核酮糖羧化酶(Rubisco)、1, 7-二磷酸景天庚酮糖酯酶(SBPase)和1, 6-二磷酸果糖醛缩酶(FBAase)活性显著提高,但转酮醇酶(TKase)活性无显著变化。表明外源H_2O_2能够通过提高PSⅡ光化学效率和碳同化关键酶活性而非依赖叶黄素循环的热耗散来减轻La胁迫导致的光抑制,从而缓解La胁迫幼苗生长的受抑程度,增强裸燕麦对La胁迫的适应性。     

减氮运筹对甘薯光合作用和叶绿素荧光特性的影响

光合性能是决定作物产量形成的关键,氮肥的合理施用是调控作物光合特性和产量形成的重要措施.于2016—2017年开展盆栽试验,研究了减氮和施肥方式对甘薯叶片光合作用和叶绿素荧光特性的影响.试验以常规习惯基施氮肥100 kg·hm^-2为对照(FP),在常规施氮量的基础上减氮20%,同时设置3种氮肥运筹方式:100%基施(JS)、100%移栽后35 d追施(KS)、50%基施+50%移栽后35 d追施(FS).结果表明:与常规基施氮肥100 kg·hm^-2相比,减氮条件下氮肥全部基施显著降低了全生育期甘薯光合性能,但追施处理显著提高了块根膨大期净光合速率(P_n)、气孔导度(g_s)、胞间CO₂浓度(C_i)和叶绿素(Chl a+b)含量.不同处理下,P_n、g_s、C_i和Chl a+b均以50%基施+50%追施处理最高.减氮分施处理甘薯块根膨大期的PSⅡ实际光化学效率(Φ_PSⅡ)、光化学淬灭系数(q_P)、PSⅡ最大光化学效率(F_v/F_m)和PSⅡ潜在活性(F_v/F_o) 提高,而初始荧光(F_o)和非光化学淬灭系数(NPQ)则降低.氮肥分施通过提高PSⅡ的光化学效率和电子传递速率,降低光能的热耗散,提高了甘薯块根膨大期功能叶的光合速率.2个品种不同年际间表现相同.表明氮肥一次性基施或追施均不利于提高甘薯叶片光合性能.减氮20%水平下,50%基施+50%追施可减缓叶片早衰,延长叶片功能期,提高甘薯的光合生产能力和生物量,有利于产量形成.     

Estimating age‐dependent survival from age‐aggregated ringing data—extending the use of historical records

Bird ring‐recovery data have been widely used to estimate demographic parameters such as survival probabilities since the mid‐20th century. However, while the total number of birds ringed each year is usually known, historical information on age at ringing is often not available. A standard ring‐recovery model, for which information on age at ringing is required, cannot be used when historical data are incomplete. We develop a new model to estimate age‐dependent survival probabilities from such historical data when age at ringing is not recorded; we call this the historical data model. This new model provides an extension to the model of Robinson, 2010, Ibis, 152, 651–795 by estimating the proportion of the ringed birds marked as juveniles as an additional parameter. We conduct a simulation study to examine the performance of the historical data model and compare it with other models including the standard and conditional ring‐recovery models. Simulation studies show that the approach of Robinson, 2010, Ibis, 152, 651–795 can cause bias in parameter estimates. In contrast, the historical data model yields similar parameter estimates to the standard model. Parameter redundancy results show that the newly developed historical data model is comparable to the standard ring‐recovery model, in terms of which parameters can be estimated, and has fewer identifiability issues than the conditional model. We illustrate the new proposed model using Blackbird and Sandwich Tern data. The new historical data model allows us to make full use of historical data and estimate the same parameters as the standard model with incomplete data, and in doing so, detect potential changes in demographic parameters further back in time.