A neutral sampling formula for multiple samples and an 'exact' test of neutrality

As the utility of the neutral theory of biodiversity is increasingly being recognized, there is also an increasing need for proper tools to evaluate the relative importance of neutral processes (dispersal limitation and stochasticity). One of the key features of neutral theory is its close link to data: sampling formulas, giving the probability of a data set conditional on a set of model parameters, have been developed for parameter estimation and model comparison. However, only single local samples can be handled with the currently available sampling formulas, whereas data are often available for many small spatially separated plots. Here, I present a sampling formula for multiple, spatially separated samples from the same metacommunity, which is a generalization of earlier sampling formulas. I also provide an algorithm to generate data sets with the model and I introduce a general test of neutrality that does not require an alternative model; this test compares the probability of the observed data (calculated using the new sampling formula) with the probability of model-generated data sets. I illustrate this with tree abundance data from three large Panamanian neotropical forest plots. When the test is performed with model parameters estimated from the three plots, the model cannot be rejected; however, when parameter estimates previously reported for BCI are used, the model is strongly rejected. This suggests that neutrality cannot explain the structure of the three Panamanian tree communities on the local (BCI) and regional (Panama Canal Zone) scale simultaneously. One should be aware, however, that aspects of the model other than neutrality may be responsible for its failure. I argue that the spatially implicit character of the model is a potential candidate.     

不同基质栽培的猴头菌子实体多糖理化性质和体外免疫活性

【背景】猴头菌多糖是猴头菌(Hericium erinaceus)中主要的活性成分,具有提高免疫力、抗肿瘤、降血糖、抗突变、抗衰老等多种功效。目前对于猴头菌多糖的研究主要集中在结构分析上,有关不同基质栽培对于猴头菌子实体多糖理化性质的影响鲜见报道。【目的】研究不同基质栽培的猴头菌子实体多糖的理化性质和体外免疫活性,筛选出高产优质猴头菌的栽培配方。【方法】采用7种不同配方的基质经工厂化栽培获得不同的猴头菌子实体,对其子实体产量和粗多糖含量进行统计和分析测定,并对7种不同基质栽培获得的猴头菌子实体多糖的分子量分布及单糖组成等理化特征进行分析,比较其对刺激RAW264.7巨噬细胞株释放NO的差异。【结果】综合各项指标表明,配方2 (木屑30%,玉米芯40%,棉籽壳15%,玉米粉2%,麸皮6%,米糠5%,石膏1%,石灰1%)和配方7 (玉米芯39%,棉籽壳10%,麸皮10%,米糠30%,大豆皮5%,甜菜渣4%,碳酸钙2%)栽培获得的猴头菌子实体具有较高的多糖含量和活性。【结论】所选配方适合作为栽培猴头菌深加工原料的培养基质。     

A precise water displacement method for estimating egg volume

ABSTRACT.   Relationships between egg volume and an array of life-history traits have been identified for many bird species. Despite the importance of egg volume and the need for precise and accurate measurements, egg volume is usually estimated using a mathematical model that incorporates length and width measurements along with a shape variable. We developed an instrument that provides precise estimates of egg volume and can be easily used in the field. Using Clapper Rail ( Rallus longirostris ) eggs, we compared egg volumes measured using our instrument with estimates based on linear measurements. We found our instrument to be both precise and accurate. Compared with a method based on linear measurements of eggs, use of our instrument reduced variation in egg volume estimates by 1.6 cm³, approximately 8% of the volume of a Clapper Rail's egg. Further advantages of our technique include ease of use, increased accuracy of field-based volume estimates, and increased resolution of variation in egg volume estimates. In addition, our technique does not require postdata collection processing time and did not influence hatching success. Also, for Clapper Rails and similar species, our technique can be combined with other techniques (e.g., egg flotation) so that both egg volume and embryonic stage can be estimated at the same time.     

补肾解毒方抗脑老化机制的体外研究

摘要 目的：探讨补肾解毒方含药血清抗脑老化的体外分子机制。方法：采用过氧化氢诱导制备人脑胶质细胞衰老模型，使用补肾解毒方含药血清干预以期达到对人脑胶质细胞衰老模型的治疗效果，CCK-8法检测细胞活力，采用β-半乳糖苷酶染色法观察衰老阳性细胞比例，活性氧荧光探针法检测胞内活性氧水平，流式细胞术检测细胞凋亡比例，qPCR检测细胞中衰老相关基因CXCL1、FOXO1、P16、IL1A、IGFBP3、IL6的转录水平。结果：补肾解毒方含药血清可显著增强细胞活力（P＜0.05），显著减少过氧化氢诱导的衰老阳性细胞比例（P＜0.05），降低活性氧水平，显著减少凋亡细胞比例（P＜0.01），下调IL1A、IL6、CXCL1、IGFBP3、FOXO1转录水平。结论：补肾解毒方含药血清可显著抑制过氧化氢诱导的人脑胶质细胞衰老，其可能与增强细胞活力、抗炎、抗凋亡、降低胞内活性氧水平等有关。     

Decompositions of Price’s formula in an inhomogeneous population structure

The central tool for the study of allele frequency change due to selection is the remarkably simple but powerful formula of Price [Nature 227 (1970) 520] . Here, I provide what might be called a structural analysis of this formula. The formula essentially accumulates the average allele frequency change over many instances of a fitness‐determining interaction, but there are different ways of organizing this average and these lead to quite different computational algorithms. I present three of these: an analysis by population state, an analysis by recipient and an analysis by actor. A comparison of these can lead to a heightened understanding of the different factors behind selective allele frequency change. In particular, I pay attention to the effects of structural inhomogeneity on reproductive value (RV) and emphasize that Price’s formula measures RV‐weighted allele frequency change. I examine in detail a simple example as a crucial way of cementing the different theoretical pathways. My aim was to produce a simple transparent presentation and therefore I work with a simple population structure and have omitted a number of technical details that are found elsewhere.     

The structure of allelic diversity in the presence of purifying selection

In the absence of selection, the structure of equilibrium allelic diversity is described by the elegant sampling formula of Ewens. This formula has helped to shape our expectations of empirical patterns of molecular variation. Along with coalescent theory, it provides statistical techniques for rejecting the null model of neutrality. However, we still do not fully understand the statistics of the allelic diversity expected in the presence of natural selection. Earlier work has described the effects of strongly deleterious mutations linked to many neutral sites, and allelic variation in models where offspring fitness is unrelated to parental fitness, but it has proven difficult to understand allelic diversity in the presence of purifying selection at many linked sites. Here, we study the population genetics of infinitely many perfectly linked sites, some neutral and some deleterious. Our approach is based on studying the lineage structure within each class of individuals of similar fitness in the deleterious mutation-selection balance. Consistent with previous observations, we find that for moderate and weak selection pressures, the patterns of allelic diversity cannot be described by a neutral model for any choice of the effective population site. We compute precisely how purifying selection at many linked sites distorts the patterns of allelic diversity, by developing expressions for the likelihood of any configuration of allelic types in a sample analogous to the Ewens sampling formula.     

Melanin Standard Method: Empirical Formula 2

Natural melanins are composed of two distinct portions; a protein fraction and a chromophoric backbone. There is no unequivocal evidence for covalent bonding between these two fractions, and standard protocols used in protein purification have failed to separate the protein fraction from the chromophoric fraction. In order to study the chromophoric backbone, many workers have resorted to harsh isolation and purification protocols that are now known to degrade and damage the chromophoric portion. These artifactual melanin preparations are poor models for valid chemical, physical, and biological studies. We have developed a mild isolation and purification protocol for melanins that takes into consideration both the particulate nature of natural melanins and the stability characteristics of the chromophoric fraction. Mathematical factoring of the quantitative amino acid data into the elemental analysis was used to obtain the empirical formula of the chromophoric backbone of melanins. The analyses have shown that melanins from various sources have significantly different amino acid compositions and contents, molar C/N ratios, and empirical formulae. This method successfully differentiates melanins from a variety of sources, namely, human hair, Sepia officinalis, Sigma Chemical Company (cat. no. M8631), autoxidation of dopa, and from the feathers of Rhode Island Red chickens. Analytical results from these studies are presented and discussed.     

活血解毒、益气养阴法治疗狼疮性血管炎临床及免疫研究

目的:观察活血解毒、益气养阴法对狼疮性血管炎临床疗效及免疫功能的影响。方法:选择系统性红斑狼疮患者60例,其中活动期伴血管炎40例,非活动期20例,同时选择20例健康人作为对照组,检测可溶性血栓调节素(sTM)、血管内皮生长因子(VEGF)的水平、抗中性粒细胞胞浆抗体(ANCA)的阳性率;并将40例活动期伴血管炎患者随机分为中西医结合治疗组(狼疮饮+常规西药)和对照组(常规西药),治疗6个月后观察临床疗效,并检测治疗前和治疗后第1,6个月sTM、VEGF、ANCA水平和阳性率变化。结果:中西医结合治疗组疗效优于对照组,治疗组治疗后sTM、VEGF、ANCA水平和阳性率下降优于对照组(P<0.05)。结论:中西医结合治疗可提高狼疮性血管炎的疗效,改善免疫功能。     

Aerial and Aquatic Respiration in the River Crab Potamonautes Warreni Calman with Notes on Gill Structure

Summary

The oxygen consumption rate (?O₂) for Potamonauteus warreni Calman (= Potamon warreni (Calman) kept in 25 °C water was 34,4 μmol 1^?1 O₂ kg^?1 and after 72 hours in 98% R.H. air the rate was 31,9 μmol 1^?1 O₂ kg^?1 min^?1. The ?O₂ values for each of the two groups are not significantly different (P > 0,05). The partial oxygen tension of pre-branchial (v = venous) haemolymph (P_vCO₂) is 15,3 mm Hg in water and 13,0 mm Hg in air); partial carbon dioxide tension of pre-branchial (v) haemolymph (P_vCO₂) is 13,2 mm Hg in water and 13,0 mm Hg in air); the total carbon dioxide concentration in pre-branchial (v) haemolymph (C_vCO₂) tot. is 12,3 mmol 1^?1 in air and 13,9 mmol 1^?1 in water) are not significantly different for the two groups (P > 0,05). The haemolymph pH and the lactate concentration for crabs in water was found to be 7,51 and 0,38 mmol 1^?1 respectively. No significant differences were found in pre-branchial haemolymph oxygen tension, carbon dioxide tension, total carbon dioxide content, haemolymph pH, lactate level, chloride concentration, P₅₀ and haemocyanin-oxygen cooperativity in control crabs kept in water, and experimental crabs held in air for 72 hours. The chloride concentration, (327,0 mmol 1^?1) for crabs kept in water does not differ from that of crabs held in air for 72 hours but is at least 15% higher than the sodium concentration (255 mmol 1^?1) for crabs kept in water. The gill surface area is 520 mm² g^?1 wet body mass; on average 9,2 gill platelets (lamellae) can be found on a gill length of one millimetre. Each lamella is spaced 60–70 μm apart, each with a thickness of 30–40 μm. It is concluded that P. warreni may be described as a truly amphibious fresh-water crab.