Use of hidden Markov capture–recapture models to estimate abundance in the presence of uncertainty: Application to the estimation of prevalence of hybrids in animal populations

Estimating the relative abundance (prevalence) of different population segments is a key step in addressing fundamental research questions in ecology, evolution, and conservation. The raw percentage of individuals in the sample (naive prevalence) is generally used for this purpose, but it is likely to be subject to two main sources of bias. First, the detectability of individuals is ignored; second, classification errors may occur due to some inherent limits of the diagnostic methods. We developed a hidden Markov (also known as multievent) capture–recapture model to estimate prevalence in free‐ranging populations accounting for imperfect detectability and uncertainty in individual's classification. We carried out a simulation study to compare naive and model‐based estimates of prevalence and assess the performance of our model under different sampling scenarios. We then illustrate our method with a real‐world case study of estimating the prevalence of wolf (Canis lupus) and dog (Canis lupus familiaris) hybrids in a wolf population in northern Italy. We showed that the prevalence of hybrids could be estimated while accounting for both detectability and classification uncertainty. Model‐based prevalence consistently had better performance than naive prevalence in the presence of differential detectability and assignment probability and was unbiased for sampling scenarios with high detectability. We also showed that ignoring detectability and uncertainty in the wolf case study would lead to underestimating the prevalence of hybrids. Our results underline the importance of a model‐based approach to obtain unbiased estimates of prevalence of different population segments. Our model can be adapted to any taxa, and it can be used to estimate absolute abundance and prevalence in a variety of cases involving imperfect detection and uncertainty in classification of individuals (e.g., sex ratio, proportion of breeders, and prevalence of infected individuals).     

Do Norwegian Atlantic salmon feed in the northern Barents Sea? Tag recoveries from 70 to 78° N

Three tagged Atlantic salmon Salmo salar were recaptured as subadults or adults (1·4–3 kg) between 70·5 and 78° N in the western Barents Sea, two of which originated from the Alta Fjord region in northern Norway and one from the Drammen River, south-eastern Norway. An additional tag was recovered from the stomach of a Greenland halibut Reinhardtius hippoglossoides captured south-west of Bear Island at >600 m depth; this tag was from a smolt released in the River Alta 1 month earlier. These are the northernmost tag recoveries reported for Atlantic salmon, and indicate that Norwegian Atlantic salmon, especially the fish from northern populations, may use the northern Barents Sea as a feeding area during part of their life cycle.     

快速IgM抗体捕捉ELISA的建立及其在乙脑早期诊断中的初步应用

用辣根过氧化物酶标记的抗日本脑炎病毒(JEV)种特异性单克隆抗体为结合物,建立了一种快速IgM抗体捕捉酶联免疫测定法(RMAC-ELISA),并初步用于乙脑的快速诊断,取得了良好的效果。该法通过用鞣酸预处理微板,提高反应温度,在稀释液中加入PEG并提高NaCl浓度,用鸡蛋清代替牛血清白蛋白或鸡血清,用自来水代替PBS作为洗液,用快速漱洗3次代替3×5分钟洗涤,用TMBS代替OPD底物,用酶标单克隆抗体代替多克隆结合物等措施,加快了反应速度,缩短了反应时间,简化了操作步骤,提高了敏感性,保证了特异性。从微板预处理至出结果,仅需1小时。由于该法具有简便、快速、特异、敏感等特性,不仅可以用于乙脑的早期诊断及实验室研究,还有可能推广到其它的免疫学检测方法中去。     

侧柏和北美香柏(柏科)的传粉机制(英)

观察了侧柏（Phaycladusorientalis（L．）Franco）和北美香柏（ThujaoccidentalisL．）散粉后花粉进入珠孔的过程。在散粉期,这两种植物的胚珠均分泌出传粉滴。当花粉落到传粉滴上后,引起传粉滴表面的形状发生改变或减弱胚珠的继续分泌,使得该传粉滴蒸腾加快,导致其比未授粉的传粉滴明显收缩。观察结果表明：不同植物的花粉导致侧柏传粉滴的收缩速率不尽相同。其中,与侧柏亲缘关系较近的植物花粉引起传粉滴的收缩速率和侧柏自身花粉引起的传粉滴收缩速率相似;反之,收缩速率变慢。侧柏传粉滴的收缩可能主要是由于花粉减弱胚珠分泌的结果。     

Optimized nLC-MS workflow for laser capture microdissected breast cancer tissue

Reliable sample preparation is of utmost importance for comparative proteome analysis, particularly when investigating minute amounts of clinical specimens, such as laser capture microdissected tumor tissue. In this study, we present an optimized nanoLC-MS workflow specifically for the analysis of laser capture microdissected breast cancer tissue. Analytical performance of different laser capture microdissection (LCM) functions available on the PALM system, time dependent trypsin digestion efficiency, effect of sample preparation and digestion time on peptide modification, semi-tryptic peptides and missed cleavages were evaluated. Our results show that microdissection from uncoated glass slides results in protein degradation; that protease and phosphatase inhibitors do not result in detectable improvement in number of peptides or semi-tryptic peptides; and that digestion time longer than four hours drastically reduces the number of missed cleavages, but also increases the number of unexpectedly modified peptides. Overalkylation was the most dominant side-reaction, which significantly increased overnight (P=0.05). The latter effect could almost completely be reverted by the use of a quenching agent (P=0.001). Taken together, our results show that it is of importance to carefully control sample handling steps so that reliable protein identification and quantitation can be performed within comparative proteomics studies using LCM. This article is part of a Special Issue entitled: Proteomics: The clinical link.     

三维基因组学研究进展

三维基因组学是一门研究基因组三维空间结构与功能的新兴学科,主要研究基因组序列在细胞核内的三维空间构象,及其对DNA复制、DNA重组、基因表达调控等生物过程的生物学效应。自染色质构象捕获技术 (3C)出现后,三维基因组学相关研究领域飞速发展。借助于3C及其衍生技术、Hi-C和ChIA-PET等技术,科学家能对各类物种的三维基因组进行更为深入的研究,从而揭示微生物、植物和动物基因组的空间构象、染色质的相互作用模式、转录调控以及不同生物学性状的形成机制;挖掘与生命活动和疾病相关的关键基因和信号通路;推动农业科学、生命科学和医学等领域的快速发展。文中就三维基因组学研究进展作一综述,主要阐述三维基因组学的概念和研究技术的发展及其在农业科学、生命科学和医学等领域的应用,尤其是肿瘤领域所取得的阶段性研究成果。     

幼年斑马鱼的视觉系统与捕食行为

神经环路的研究是揭示动物行为神经机制的关键。斑马鱼作为一种低等脊椎动物, 在神经环路的研究中有着独特优势。文章描述了斑马鱼视觉系统及其下游的神经环路, 重点讨论了它们在捕食行为中的可能作用。斑马鱼捕食行为主要依赖于视觉功能, 该过程涉及到视觉-运动通路各个层次的神经环路, 包括下游的网状脊髓命令神经元、脊髓内部的运动控制环路以及一些亟待研究的功能单元。随着在体记录和操纵神经元活动技术的成熟, 以及行为学范式的完善, 对斑马鱼捕食行为相关神经环路的研究将在未来数年内迅速发展, 同时也将推动神经科学相关研究的进步。     

Effect of starvation time on the prey capture behaviour, functional response and population growth of Asplanchna sieboldi (Rotifera)

1. We examined the effect of different periods of prior starvation(from 30 min to 16 h) on the prey capture behaviour, and functional and numerical responses of the predatory rotifer Asplanchna sieboldi using the rotifer Brachionus calyciflorus as prey.
2. Feeding activity (i.e. encounter, attack, capture and ingestion) by Asplanchna increased significantly with increasing prey densities from 2 to 16 mL⁻⁻¹ and with increasing prior starvation periods from 0.5 to 8 h.
3.  Asplanchna sieboldi showed a type II functional response at all the prior starvation periods tested. The asymptotic prey density was highest after 8 h of starvation.
4. The instantaneous population growth rate of A. sieboldi ranged from 0.089 ± 0.044 (when starved for 8 h in every 24 h and at a prey density of 2 individuals mL⁻⁻¹ for the other 16 h) to 1.015 ± 0.142 in the control (no starvation and at a prey density of 16 individuals mL⁻⁻¹). The effect of starvation time on the numerical response was evident only at the higher prey density.     

哺乳动物单细胞研究技术的现状与未来

近年来,生命科学和医学的基础研究已深入到单细胞阶段。单细胞研究为揭示生命活动的基本规律、探索细胞异质性、提高对疾病发病机制的认识等提供了重要的线索和依据,同时,单细胞技术已被应用于日常实践中,如法医学和临床生殖医学。单细胞研究中使用的技术也在不断变化,并越来越复杂。文中主要介绍单细胞分离技术,包括手工挑取、激光捕获显微切割和微流控技术,以及单细胞中DNA、RNA和蛋白质分析方法的各种技术。此外,文中总结了近年来生命科学和医学领域的主要单细胞研究成果,讨论了单细胞相关技术和研究的不足,并介绍了其未来的发展方向。