Estimation of parameters in large offspring number models and ratios of coalescence times

The ratio of singletons to the total number of segregating sites is used to estimate a reproduction parameter in a population model of large offspring numbers without having to jointly estimate the mutation rate. For neutral genetic variation, the ratio of singletons to the total number of segregating sites is equivalent to the ratio of total length of external branches to the total length of the gene genealogy. A multinomial maximum likelihood method that takes into account more frequency classes than just the singletons is developed to estimate the parameter of another large offspring number model. The performance of these methods with regard to sample size, mutation rate, and bias, is investigated by simulation. The expected value of the ratio of the total length of external branches to the total length of the whole tree is, using simulation, shown to decrease for the Kingman coalescent as sample size increases, but can increase or decrease, depending on parameter values, for Λ coalescents. Considering ratios of tree statistics, as opposed to considering lengths of various subtrees separately, can yield better insight into the dynamics of gene genealogies.     

Ligand binding induces a conformational change in ifnar1 that is propagated to its membrane-proximal domain

The type I interferon (IFN) receptor plays a key role in innate immunity against viral and bacterial infections. Here, we show by intramolecular Förster resonance energy transfer spectroscopy that ligand binding induces substantial conformational changes in the ectodomain of ifnar1 (ifnar1-EC). Binding of IFNα2 and IFNβ induce very similar conformations of ifnar1, which were confirmed by single-particle electron microscopy analysis of the ternary complexes formed by IFNα2 or IFNβ with the two receptor subunits ifnar1-EC and ifnar2-EC. Photo-induced electron-transfer-based fluorescence quenching and single-molecule fluorescence lifetime measurements revealed that the ligand-induced conformational change in the membrane-distal domains of ifnar1-EC is propagated to its membrane-proximal domain, which is not involved in ligand recognition but is essential for signal activation. Temperature-dependent ligand binding studies as well as stopped-flow fluorescence experiments corroborated a multistep conformational change in ifnar1 upon ligand binding. Our results thus suggest that the relatively intricate architecture of the type I IFN receptor complex is designed to propagate the ligand binding event to and possibly even across the membrane by conformational changes.     

Tertiary structure and carbohydrate recognition by the chitin-binding domain of a hyperthermophilic chitinase from Pyrococcus furiosus

A chitinase is a hyperthermophilic glycosidase that effectively hydrolyzes both α and β crystalline chitins; that studied here was engineered from the genes PF1233 and PF1234 of Pyrococcus furiosus. This chitinase has unique structural features and contains two catalytic domains (AD1 and AD2) and two chitin-binding domains (ChBDs; ChBD1 and ChBD2). A partial enzyme carrying AD2 and ChBD2 also effectively hydrolyzes crystalline chitin. We determined the NMR and crystal structures of ChBD2, which significantly enhances the activity of the catalytic domain. There was no significant difference between the NMR and crystal structures. The overall structure of ChBD2, which consists of two four-stranded β-sheets, was composed of a typical β-sandwich architecture and was similar to that of other carbohydrate-binding module 2 family proteins, despite low sequence similarity. The chitin-binding surface identified by NMR was flat and contained a strip of three solvent-exposed Trp residues (Trp274, Trp308 and Trp326) flanked by acidic residues (Glu279 and Asp281). These acidic residues form a negatively charged patch and are a characteristic feature of ChBD2. Mutagenesis analysis indicated that hydrophobic interaction was dominant for the recognition of crystalline chitin and that the acidic residues were responsible for a higher substrate specificity of ChBD2 for chitin compared with that of cellulose. These results provide the first structure of a hyperthermostable ChBD and yield new insight into the mechanism of protein-carbohydrate recognition. This is important in the development of technology for the exploitation of biomass.     

Function of plastoquinone in heat stress reactions of plants

The effect of high temperature treatment (40 °C, 3 h, illumination at 100 μmol m^− 2 s^− 1) on the photosynthetic electron flow in barley seedlings of different age was investigated. Thermoinduced inhibition of the liner electron flow due to partial impairment of the water oxidizing complex (WOC) and the increase in the extent of Q_A⁻ reoxidation by Tyr_z^ox in thylakoids isolated from 4-day-old leaves was shown by measurements of oxygen evolution using benzoquinone or potassium ferricyanide as electron acceptors, as well as by following Q_A⁻ reoxidation kinetics in the absence and presence of exogenous electron acceptors, DCBQ and DMBQ. Using HPLC analysis, an increase in the oxidation of the photoactive plastoquinone pool in young leaves under heating was shown. In older, 11-day-old leaves, heat treatment limited both photosynthetic electron flow and oxygen evolution. The same effects of heat shock on oxygen evolution caused an inhibition of electron flow on the donor side of PSII only. However, a rise in the proportion of PSII with Q_A⁻ reoxidized through recombination with the S₂/S₃ state of the WOC was observed. The addition of exogenous electron acceptors (DCBQ and DMBQ) and a donor (DPC) showed that the thermoinduced decrease in the electron transport rate was caused by an impediment of electron flow from Q_A⁻ to acceptor pool. The decrease in size of the photoactive PQ-pool and a change in the proportions of oxidized and reduced PQ in older leaves under heat treatment were shown. It was suggested that a thermoinduced change of the redox state of the PQ-pool and a redistribution of plastoquinone molecules between photoactive and non-photoactive pools are the mechanisms which reflect and regulate the response of the photosynthetic apparatus under heat stress conditions.     

Allosterically coupled calcium and magnesium binding sites are unmasked by ryanodine receptor chimeras

We studied cation regulation of wild-type ryanodine receptor type 1 (_WTRyR1), type 3 (_WTRyR3), and RyR3/RyR1 chimeras (Ch) expressed in 1B5 dyspedic myotubes. Using [³H]ryanodine binding to sarcoplasmic reticulum (SR) membranes, Ca²⁺ titrations with _WTRyR3 and three chimeras show biphasic activation that is allosterically coupled to an attenuated inhibition relative to _WTRyR1. Chimeras show biphasic Mg²⁺ inhibition profiles at 3 and 10 μM Ca²⁺, no observable inhibition at 20 μM Ca²⁺ and monophasic inhibition at 100 μM Ca²⁺. Ca²⁺ imaging of intact myotubes expressing Ch-4 exhibit caffeine-induced Ca²⁺ transients with inhibition kinetics that are significantly slower than those expressing _WTRyR1 or _WTRyR3. Four new aspects of RyR regulation are evident: (1) high affinity (H) activation and low affinity (L) inhibition sites are allosterically coupled, (2) Ca²⁺ facilitates removal of the inherent Mg²⁺ block, (3) _WTRyR3 exhibits reduced cooperativity between H activation sites when compared to _WTRyR1, and (4) uncoupling of these sites in Ch-4 results in decreased rates of inactivation of caffeine-induced Ca²⁺ transients.     

Correlation of neutrophil and monocyte derived interleukin-1 receptor antagonist and interleukin-8 with colitis severity in the rabbit

Activated neutrophils and monocytes produce interleukin (IL)-8, a pro-inflammatory chemokine, but also IL-1 receptor antagonist (IL-1ra), which is an anti-inflammatory cytokine. We were interested to see the profiles of IL-8 and IL-1ra in the colonic tissue and in the peripheral blood leukocytes (PBL) during the development of immune complex induced colitis in rabbits. IL-1ra and IL-8 in PBL were measured in 26 rabbits at time 0 h, 24 h, and 48 h after induction of colitis. The colons were removed at 48 h for measuring myeloperoxidase (MPO), ulcer area, IL-1ra and IL-8. Epithelial damage, crypt abscess formation and leukocyte infiltration of the colonic tissue were major features of this colitis model. During the development of colitis, there was an increase in circulating neutrophils and monocytes (P < 0.0001), but not lymphocytes. Likewise, elevated amounts of IL-1ra (P = 0.0001) and IL-8 (P = 0.0219) production by PBL were observed following induction of colitis. Flow cytometry revealed major source of IL-1ra was monocytes, while the main sources of IL-8 were neutrophils and monocytes. There was correlation between MPO and ulcer area (R_s = 0.6327, P < 0.0001). At 24 h, PBL from MPO^High group (n = 11) showed increased IL-1ra (P = 0.027) and IL-8 (P = 0.0128) levels vs MPO^Low group (n = 15). IL-8 production by PBL showed correlation with tissue MPO (R_s = 0.4273, P = 0.0295). The colitis in this model was associated with an increase in circulating monocytes and neutrophils, which released increased amounts of IL-8 and IL-1ra. Further, IL-8 and IL-1ra showed correlation with the severity of colitis. These observations should significantly further understandings on the role of neutrophils and monocytes in the immunopathogenesis of ulcerative colitis.     

氮、磷、钾肥配施对桂花品种'金玉台阁'开花性状及叶片中叶绿素和营养元素含量的影响

以桂花品种'金玉台阁'(Osmanthus fragrans'Jinyu Taige')盆栽苗为供试材料,采用"3414"肥料效应试验设计方案,研究了不同单株施用量CO(NH2)2(0.0、1.0、2.0和3.0 g)、NH4H2PO4(0.0、1.5、3.0和4.5 g)和KCl(0.0、0.5、1.0、1.5 g)对秋冬生长期(2014年10月至2015年2月)'金玉台阁'开花性状及叶片中叶绿素和营养元素的影响进行了比较和分析,并筛选出适宜的氮、磷、钾肥施用量.结果表明:与CK〔CO(NH2)2、NH4H2PO4和KCl的单株施用量均为0.0 g〕组相比,各氮、磷、钾肥配施处理组'金玉台阁'的单株产花量、花瓣相对含水量、花径以及叶片中叶绿素、全氮、全磷和全钾的含量总体上显著升高.CO(NH2)2单株施用量对'金玉台阁'单株产花量、叶片中叶绿素含量和全氮含量的影响最大,NH4H2PO4单株施用量对这3个指标的影响次之;NH4H2PO4单株施用量对'金玉台阁'叶片中全磷含量的影响最大;KCl单株施用量对'金玉台阁'花瓣相对含水量、花径及叶片中全钾含量的影响最大.在秋冬生长期内叶片中叶绿素含量呈先降低后升高的趋势,均在12月份降至最低值.通过建立'金玉台阁'单株产花量(y)与CO(NH2)2、NH4 H2 PO4和KCl的单株施用量(分别为xN、xP和xK)间的肥料效应模型,得到的三元二次肥料效应模型为y=1.2027+0.7561×xN+0.2632×xP+0.4590×xK-0.2761×xN2-0.1201×xP2-0.5007×xK2+0.1901×xN×xP-0.0960×xN×xK+0.1185×xP×xK.以单株产花量为目标,'金玉台阁'的CO(NH2)2、NH4 H2 PO4和KCl的最佳单株施用量分别为2.58、3.56和0.86 g.     

岷江上游不同树种林地客土混合对土壤生物化学性质和枯落叶分解的影响

人工纯林的长期经营会引发连栽障碍,影响森林的可持续发展,解决途径是引进更新树种形成混交林。为了指导四川岷江上游人工纯林更新树种和混交比例的选择,尝试通过针阔叶树种林地腐殖质土壤及其枯落物的客置和混合原位培养试验,探讨不同树种种间关系的协调性。结果表明:(1)连香树、云南松和云杉林地经过各种客土混合后酶活性普遍都有所提高,而在糙皮桦林地,经云南松土壤客土混合后酶活性普遍有所下降,经云杉土壤客土混合后脲酶和过氧化氢酶活性有不同程度的提高,蔗糖酶活性却有所下降;(2)连香树和云南松林地经过各种客土混合后,加速了C和N由枯落物进入土壤,而在糙皮桦和云杉林地经过各种客土混合后,促进了N从枯落物和有机质矿化分解进入土壤的过程,但却会对有机C进入土壤产生抑制作用;(3)所有不同针阔叶树种林地经土壤客土混合后,对原有土壤的酸碱性起到中和的作用,即原来的阔叶林地土壤向偏酸性方向发展,而原来的针叶林地土壤向偏碱性方向发展;(4)所有不同树种林地的客土混合对枯落叶分解均具有明显的促进作用;(5)连香树林地的LM0.15~0.50和LY0.15~0.35、糙皮桦林地的HM0.15和HY0.15~0.50、云南松林地的ML0.15~0.50和MH0.35~0.50、云杉林地的YL0.35~0.50和YH0.35类型是相对较好的选择,可作为确定更新树种和混交比例的参考。