Using dynamic N‐mixture models to test cavity limitation on northern flying squirrel demographic parameters using experimental nest box supplementation

Dynamic N‐mixture models have been recently developed to estimate demographic parameters of unmarked individuals while accounting for imperfect detection. We propose an application of the Dail and Madsen ( 2011 : Biometrics, 67 , 577–587) dynamic N‐mixture model in a manipulative experiment using a before‐after control‐impact design (BACI). Specifically, we tested the hypothesis of cavity limitation of a cavity specialist species, the northern flying squirrel, using nest box supplementation on half of 56 trapping sites. Our main purpose was to evaluate the impact of an increase in cavity availability on flying squirrel population dynamics in deciduous stands in northwestern Québec with the dynamic N‐mixture model. We compared abundance estimates from this recent approach with those from classic capture–mark–recapture models and generalized linear models. We compared apparent survival estimates with those from Cormack–Jolly–Seber (CJS) models. Average recruitment rate was 6 individuals per site after 4 years. Nevertheless, we found no effect of cavity supplementation on apparent survival and recruitment rates of flying squirrels. Contrary to our expectations, initial abundance was not affected by conifer basal area (food availability) and was negatively affected by snag basal area (cavity availability). Northern flying squirrel population dynamics are not influenced by cavity availability at our deciduous sites. Consequently, we suggest that this species should not be considered an indicator of old forest attributes in our study area, especially in view of apparent wide population fluctuations across years. Abundance estimates from N‐mixture models were similar to those from capture–mark–recapture models, although the latter had greater precision. Generalized linear mixed models produced lower abundance estimates, but revealed the same relationship between abundance and snag basal area. Apparent survival estimates from N‐mixture models were higher and less precise than those from CJS models. However, N‐mixture models can be particularly useful to evaluate management effects on animal populations, especially for species that are difficult to detect in situations where individuals cannot be uniquely identified. They also allow investigating the effects of covariates at the site level, when low recapture rates would require restricting classic CMR analyses to a subset of sites with the most captures.     

The ImageJ ecosystem: Open‐source software for image visualization,processing, and analysis

For decades, biologists have relied on software to visualize and interpret imaging data. As techniques for acquiring images increase in complexity, resulting in larger multidimensional datasets, imaging software must adapt. ImageJ is an open‐source image analysis software platform that has aided researchers with a variety of image analysis applications, driven mainly by engaged and collaborative user and developer communities. The close collaboration between programmers and users has resulted in adaptations to accommodate new challenges in image analysis that address the needs of ImageJ's diverse user base. ImageJ consists of many components, some relevant primarily for developers and a vast collection of user‐centric plugins. It is available in many forms, including the widely used Fiji distribution. We refer to this entire ImageJ codebase and community as the ImageJ ecosystem. Here we review the core features of this ecosystem and highlight how ImageJ has responded to imaging technology advancements with new plugins and tools in recent years. These plugins and tools have been developed to address user needs in several areas such as visualization, segmentation, and tracking of biological entities in large, complex datasets. Moreover, new capabilities for deep learning are being added to ImageJ, reflecting a shift in the bioimage analysis community towards exploiting artificial intelligence. These new tools have been facilitated by profound architectural changes to the ImageJ core brought about by the ImageJ2 project. Therefore, we also discuss the contributions of ImageJ2 to enhancing multidimensional image processing and interoperability in the ImageJ ecosystem.     

国家公园生态系统生产总值核算——以海南热带雨林国家公园为例

海南热带雨林国家公园拥有我国最具代表性、连片面积最大的热带雨林,生态产品丰富,在开展国家公园生态产品价值实现机制探索上具有得天独厚的优势。本研究基于《陆地生态系统生产总值(GEP)核算技术指南》框架,构建符合热带雨林国家公园特色的GEP核算体系,对2019年海南热带雨林国家公园GEP进行核算。结果表明: 2019年,海南热带雨林国家公园GEP为2045.13亿元,单位面积GEP为0.46亿元·km^-2。其中,物质产品价值为48.50亿元,占国家公园GEP总量的2.4%;生态系统调节服务价值为1688.91亿元,占82.6%;文化服务价值为307.72亿元,占15.0%。从不同生态系统类型来看,以山地雨林、低地雨林、落叶季雨林、热带云雾林等为代表的热带雨林生态系统的单位面积价值量远高于人工林及其他生态系统,表明热带雨林生态系统在提供生态系统服务功能方面具有显著作用。此外,本研究还基于国家公园GEP核算结果,提出进一步探索生态产品价值实现路径和实现机制的相关建议。     

国家公园生态系统完整性的内涵及评价框架: 以东北虎豹国家公园为例

保护自然生态系统的完整性是我国建立国家公园的主要目标之一, 《国家公园设立规范》(GB/T 39737-2021)已将生态系统完整性作为国家公园的准入条件生态重要性的认定指标之一, 但目前对国家公园生态系统完整性的内涵还没有统一定义, 并缺乏具体的评价体系。本文在国内外相关研究的基础上, 结合我国国家公园体制试点成果及第一批国家公园设立实践, 提出了国家公园生态系统完整性的基本内涵及评价指标体系, 以期为今后设立国家公园时划定边界范围或评估国家公园管理成效提供理论依据。作者提出, 应从生态系统结构和过程完整性、功能完整性、空间格局完整性3个维度对我国国家公园生态系统完整性进行综合评价。以东北虎豹国家公园为例, 体制试点以来, 东北虎(Panthera tigris altaica)和东北豹(P. pardus orientalis)等顶级食肉动物的食物链相对完整, 虎、豹野生种群从俄罗斯进入、定居、繁衍、扩散的路径清晰, 种群稳定增长、栖息地质量持续改善, 生物多样性日益丰富, 国家公园正式设立范围划定时充分考虑了生态系统完整性保护, 生态系统完整性评级为优秀, 为国家公园可持续发展奠定了良好基础。     

Smad3 contributes to positioning of proliferating cells in colonic crypts by inducing EphB receptor protein expression

In prion diseases cellular prion protein (PrP^C) undergoes conformational transition into the β-sheet-rich form (PrP^Sc). PrP^C consists of the disordered N-terminal part and a C-terminal globular domain containing three α-helices (H1, H2, H3) and an antiparallel beta sheet (B1, B2). B2–H2 loop, which has a focal role in the species barrier, contains the highest density of asparagine (N) and glutamine (Q) residues in the whole sequence. Q/N-rich domains are essential for the conversion of yeast prions. We investigated the role of Q/N residues in the B2–H2 loop in PrP conversion. We prepared mouse PrP mutants with increasing number of consecutive Q/N residues in the B2–H2 loop. Stability of the mutants decreased with the increasing number of inserted glutamines. In vitro conversion of mutants yielded fibrils of similar morphology as the wild-type PrP. Q/N mutants accelerated fibrillization in comparison to the wild-type PrP, with mutant containing the most glutamines having the shortest lag phase. The effect of Q/N residues was specific for the B2–H2 loop and was not due to simple increase in flexibility as the introduction of Gly-Ser or Ala residues slowed the conversion despite their decreased stability. Our results thus suggest that Q/N residues in the B2–H2 loop of PrP promote protein conversion and may represent a link to conversion of Q/N-rich prions.     

Analysis of the human HP1 interactome reveals novel binding partners

Heterochromatin protein 1 (HP1) has first been described in Drosophila as an essential component of constitutive heterochromatin required for stable epigenetic gene silencing. Less is known about the three mammalian HP1 isotypes CBX1, CBX3 and CBX5. Here, we applied a tandem affinity purification approach coupled with tandem mass spectrometry methodologies in order to identify interacting partners of the mammalian HP1 isotypes. Our analysis identified with high confidence about 30–40 proteins co-eluted with CBX1 and CBX3, and around 10 with CBX5 including a number of novel HP1-binding partners. Our data also suggest that HP1 family members are mainly associated with a single partner or within small protein complexes composed of limited numbers of components. Finally, we showed that slight binding preferences might exist between HP1 family members.     

The plant cell death suppressor Adi3 interacts with the autophagic protein Atg8h

The tomato AGC protein kinase Adi3 is known to function as a suppressor of PCD and silencing of Adi3 leads to spontaneous cell death on leaves and stems. In an effort to isolate Adi3 interacting proteins, a yeast two-hybrid screen was carried out and identified the autophagy protein Atg8h as an Adi3 interactor. This interaction occurred independent of the kinase activity status of Adi3. Silencing of genes involved in autophagy is known to eliminate the restriction of pathogen-induced PCD to a few cells and leads to run away PCD. Cosilencing Adi3 with several autophagy genes lead to the same run away cell death suggesting Adi3 may be involved in autophagic regulation of PCD.     

The Open Microcirculation in Human Spleens: A Three-Dimensional Approach

It has long been debated whether the red pulp of human spleens harbors an open or a closed microcirculation or both. To solve this issue, the authors differentially stained the endothelium in red pulp arterial microvessels and in venous sinuses using brightfield and fluorescence immunohistology with reagents against CD34 and CD141. Three-dimensional models of red pulp arterial microvessels and sinuses were derived from serial double-stained paraffin sections with the help of license-free open-access software. In each model, arterial microvascular ends were traced and verified by reference to the original serial sections. In total, 142 ends were analyzed in the specimens of three individuals. None of these ends was connected to a sinus, suggesting that the human splenic red pulp harbors an entirely open circulatory system. Thus, the spleen is the only human organ where blood passes through spaces not lined by endothelia or other barrier-forming cells.     

基于功能分类的城市湿地公园景观格局--以西溪湿地公园为例

以西溪国家湿地公园为研究案例,从景观功能分类入手,揭示城市湿地公园景观格局与功能特征。结果表明:(1)西溪湿地公园是以生态保护为主,兼顾合理利用为基本功能特征,其生态保护功能区面积占整个公园的53.7%,旅游休闲区面积占46.3%;(2)西溪湿地公园生态保护功能斑块在整个公园中所占面积为42.08%,且面积大、形状复杂、多样性较低;旅游休闲斑块面积占25.41%,并且表现为斑块面积小、形状规则、多样性高等特点;(3)西溪湿地公园生态保护廊道面积是旅游休闲廊道面积的一半左右,其网络结构比旅游休闲廊道复杂,有利于生态保护功能的发挥;(4)生态保护廊道缓冲区内主要由生态保护斑块组成,旅游休闲廊道的缓冲区内生态功能斑块和旅游休闲斑块所占面积相差不大。基于功能分类的景观格局研究方法有利于识别景观功能的空间特征,能够有效揭示景观生态保护与利用的空间关系。     

准格尔黄土丘陵沟壑区杜松疏林特征分析

对内蒙古准格尔黄土丘陵沟壑区天然杜松疏林进行了林分胸径、株高、密度和群落结构等的调查.结果表明:发育良好的杜松疏林具有明显的乔木层、灌木层和草本层,如杜松-虎榛子-日阴菅群落、杜松-黄刺玫-日阴菅群落、杜松-黄刺玫-黄囊苔群落;若干扰进一步减弱,它们会演替为辽东栎+杜松或油松+杜松群落;若干扰加强,杜松疏林会逆向演替为灌丛或草原,甚至为裸沟坡地.杜松疏林有高的物种丰富度,但生境脆弱,且林分平均胸径、平均高、密度均较小,故不适合作为用材林,应作为水土保持林和种源林加以保护利用更为合理.