Metabarcoding as a tool for investigating arthropod diversity in Nepenthes pitcher plants

The biodiversity of tropical forests consists primarily of small organisms that are difficult to detect and characterize. Next‐generation sequencing (NGS) methods can facilitate analyses of these arthropod and microbial communities, leading to a better understanding of existing diversity and factors influencing community assembly. The pitchers of carnivorous pitcher plants often house surprisingly discrete communities and provide ideal systems for analysis using an NGS approach. The plants digest insects in order to access essential nutrients while growing in poor soils; however, the pitchers are also home to communities of living organisms, called inquilines. Certain arthropods appear to have coevolved with their pitcher plant hosts and are not found in other environments. We used Illumina amplicon sequencing of 18S rDNA to characterize the eukaryotes in three species of Nepenthes (Nepenthaceae) pitcher plants – N. gracilis, N. rafflesiana and N. ampullaria – in each of three different parks in Singapore. The data reveal an unexpected diversity of eukaryotes, significant differences in community diversity among host species, variation in host specificity of inquilines and the presence of gregarine parasites. Counts of whole inquiline arthropods from the first collection year were roughly correlated with scaled 18S sequence abundances, indicating that amplicon sequencing is an effective means of gauging community structure. We barcoded a subset of the dipteran larvae using COI primers, and the resulting phylogenetic tree is mostly congruent with that found using the 18S locus, with the exception of one of five morphospecies. For many 18S and COI sequences, the best BLASTn matches showed low sequence identity, illustrating the need for better databases of Southeast Asian dipterans. Finally, networks of core arthropods and their host species were used to investigate degree of host specificity across multiple hosts, and this revealed significant specialization of certain arthropod fauna.     

Additive partitioning of reef fish diversity variation: a promising marine biodiversity management tool

Additive partitioning was applied to variation in reef fish spatial diversity at Isla Isabel National Park, Nayarit state, Mexico, and to identify the environmental and spatial variables that best explains it. Analyses included expected and observed species curves, rare species analysis, additive partitioning of alpha- and beta-diversity, and canonical redundancy analysis. A total of 10,517 individuals were recorded from 75 species and 33 reef fish families, representing 85% of expected richness. Species richness beta-diversity was dependent on the site scale, while the alpha-diversity of the Shannon diversity was most significant at the transect scale. Canonical partitioning showed species richness and Shannon diversity was explained by spatially-structured environmental components. Variation in species composition and abundance was explained by a purely environmental component. Therefore, elements of habitat structure (especially corals), topographic complexity, and refuge availability determine fish species diversity. Our results suggest that greater emphasis is required to conserve sites that promote β-diversity, increasing fish spatial diversity. In Isla Isabel, these sites would be mostly those located at eastern and southern of protected sides, where coral reef patches are well represented. The results of this multi-scale analysis are valuable and useful as an addition and complement to the holistic management strategies implemented at Isla Isabel.     

天童国家森林公园树种多样性的加性分配

根据物种丰富度、Shannon指数和Simpson指数建立的物种多样性分配方法,提出分异度系数,对天童森林公园内不同森林类型的树种多样性进行了分析.结果表明,基于物种丰富度指数,总体的多样性只有小部分归功于样方内多样性,而多样性大多分配在样方间、亚群丛间或群丛间,例如在木荷-栲树群丛中,样方内只贡献了20.3%的物种丰富度.而在Shannon指数和Simpson指数中,多样性大多分配在样方内.这种差异主要是由于后两种指数不仅考虑了物种的存在与否,也考虑了其在样方内的多度.同时比较分析了加性分配与传统方法的结果.     

Mathematical modeling as a tool for investigating cell cycle control networks

Although not a traditional experimental "method," mathematical modeling can provide a powerful approach for investigating complex cell signaling networks, such as those that regulate the eukaryotic cell division cycle. We describe here one modeling approach based on expressing the rates of biochemical reactions in terms of nonlinear ordinary differential equations. We discuss the steps and challenges in assigning numerical values to model parameters and the importance of experimental testing of a mathematical model. We illustrate this approach throughout with the simple and well-characterized example of mitotic cell cycles in frog egg extracts. To facilitate new modeling efforts, we describe several publicly available modeling environments, each with a collection of integrated programs for mathematical modeling. This review is intended to justify the place of mathematical modeling as a standard method for studying molecular regulatory networks and to guide the non-expert to initiate modeling projects in order to gain a systems-level perspective for complex control systems.     

siRNA as a tool for investigating organogenesis: The pitfalls and the promises

Removing the function of a specific gene from a developing organ, by making a ‘knockout’ mouse, is a powerful method for analyzing the molecular pathways that control organogenesis. The technique is expensive, though, in terms of time and money, and complex strategies for producing conditional knockouts are needed for genes that are essential for early development of the embryo, for which an unconditional knockout would be lethal before the organ of interest begins to form. Small interfering RNAs (siRNAs) offer a method of knocking down the expression of specific genes with no need for genomic manipulation. Almost as soon as they had been discovered, siRNAs began to be used to explore the molecular biology of mammalian cells in conventional, two-dimensional culture. They have now also been applied successfully, by several groups, to knock down specific genes in various organ rudiments developing in organ culture. This article reviews the basic technique of siRNA-mediated gene knockdown and how it is being applied to organ culture. It also reviews some of the current problems and challenges in the field, and the ways in which these problems are likely to be overcome.Key words: siRNA, RNAi, organ culture, organogenesis, organ development, 3D culture     

Additive partitioning of butterfly diversity in a fragmented landscape: importance of scale and implications for conservation

Aim Most of the Atlantic Forest in Brazil occurs in fragments of various sizes. Previous studies indicate that forest fragmentation affects fruit‐feeding butterflies. Conservation strategies that seek to preserve organisms that are distributed in high‐fragmented biomes need to understand the spatial distribution of these organisms across the landscape. In view of the importance of understanding the fauna of these forest remnants, the objective of the present work is to investigate the extent to which the diversity of this group varies across spatial scales ranging from within‐forest patches to between landscapes. Location South America, south‐eastern Brazil, São Paulo State. Methods We used bait traps to sample fruit feeding butterflies at 50 points in 10 fragments in two different landscapes during a period of 12 months. Total species richness and Shannon index were partitioned additively in diversity at trap level, and beta diversity was calculated among traps, among forest patches, and between landscapes. We used permutation tests to compare these values to the expected ones under the null hypothesis that beta diversity is only a random sampling effect. Results There was significant beta diversity at the smallest scale examined; however, the significance at higher scales depends on the diversity measurement used. Beta diversity with Shannon index was smaller than expected by chance among fragments, whereas species richness was not. Among landscapes, only beta diversity in richness was higher than expected by chance. Main conclusions The results observed occur because there is great variability in species composition among forest patches in the same landscape, changing this diversity even though the communities are formed from the same pool of species. At the largest scale evaluated (between landscapes), these pattern changes and differences in beta diversity in richness were detectable. This difference is probably caused by the presence of rare species. Thus, a conservation strategy that seeks to preserve as many species as possible per unit of area in high‐fragmented biomes should give priority to protecting fragments in different landscapes, rather than more fragments in the same landscape.     

Electronic structure calculations as a tool for investigating acyl migrations in ester saponins

The possibility of acyl migrations in ester saponins from Maesa lanceolata was investigated by molecular mechanics and electronic structure calculations carried out on the major constituent maesasaponin IV3 (3beta-O-[[alpha-L-rhamnopyranosyl-(1-->2)-[beta-D-galactopyranosyl-(1-->3)]-[beta-D-galactopyranosyl-(1-->2)]-beta-D-gluco-pyranuronyl]-21beta-angeloyloxy-22alpha-propanoyloxy-13beta,28-oxido-olean-16alpha, 28alpha-diol). It was confirmed that acyl migrations could occur in rings D and E of maesasaponins.     

Additive diversity partitioning in palaeobiology: revisiting Sepkoski’s question

Abstract: Using Whittaker’s concepts of alpha, beta, and gamma diversity, Sepkoski asked how global diversity was assembled at scales ranging from the community to the province. In the years since, ecologists have recast diversity in terms of additive partitions where total diversity can be decomposed into sample‐level alpha diversity plus the sum of a series of beta diversity terms that reflect progressively larger spatial scales. Given that marine alpha diversity represents a tiny fraction of global diversity, Phanerozoic global diversity patterns must be dominated by changes in beta diversity at one or more scales. A ballooning ecological literature demonstrates wide variation in beta diversity among ecosystems, regions, and taxa, suggesting that large changes in beta diversity on evolutionary timescales are likely. But the question is which scales are the most important. Several recent palaeontological studies help to constrain beta diversity within sedimentary basins, and the emergence of sample‐based databases puts an answer to Sepkoski’s question within reach. A new method for calculating diversity partitions for richness is introduced, which allows the calculation of each species’ contribution to alpha and beta diversity, as well as the contribution of each sampling unit to beta diversity.     

Droplet digital PCR as a tool for investigating dynamics of cryptic symbionts

Interactions among symbiotic organisms and their hosts are major drivers of ecological and evolutionary processes. Monitoring the infection patterns among natural populations and identifying factors affecting these interactions are critical for understanding symbiont–host relationships. However, many of these interactions remain understudied since the knowledge about the symbiont species is lacking, which hinders the development of appropriate tools. In this study, we developed a digital droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an undescribed agamococcidian symbiont. We show that the method gives precise and reproducible results and enables detecting cryptic symbionts in low target concentration. We further exemplify the assay''s use to survey seasonally sampled natural host (Pygospio elegans) populations for symbiont infection dynamics. We found that symbiont prevalence differs spatially but does not show seasonal changes. Infection load differed between populations and was low in spring and significantly increased towards fall in all populations. We also found that the symbiont prevalence is affected by host length and population density. Larger hosts were more likely to be infected, and high host densities were found to have a lower probability of infection. The observed variations could be due to characteristics of both symbiont and host biology, especially the seasonal variation in encounter rates. Our findings show that the developed ddPCR assay is a robust tool for detecting undescribed symbionts that are otherwise difficult to quantify, enabling further insight into the impact cryptic symbionts have on their hosts.     

In vitro fertilization as a tool for investigating sexual reproduction of angiosperms

In vitro fertilization (IVF) of isolated male and female gametes of flowering plants was first accomplished in the last decade. Successful isolation of male and female gametes, and culturing of in vitro zygotes to form new plants, is a prelude to the use of IVF for research into the cellular and molecular control of fertilization in higher plants and its application as a tool in biotechnology. Genes unique to male and female gametes and zygotes of higher plants, although currently incompletely characterized, are expected to permit direct molecular dissection of fertilization. By applying IVF and microculture to zygotes and endosperm obtained by both in vivo and in vitro methods, newly activated fusion products may be observed and manipulated in media where they are directly accessible to the techniques of molecular cell biology. IVF and zygote culture may also offer potential for creating new hybrid plants by fusing isolated gametes from different species to produce unique zygotes and ultimately plants that would be impossible to obtain using typical crossing techniques. Transformation and regeneration frequencies using IVF may also be high enough to avoid the necessity of adding controversial antibiotic and herbicide resistant genes to screen transformed products. This review describes advances using IVF in plant sexual reproduction and discusses its potential in the genetic improvement of flowering plants.     

Photochemistry as a tool in investigating ionic channels: Photoaffinity probes

TPMP is a noncompetitive inhibitor of the nicotinic acetycholine receptor which blocks agonist-induced ion flux by directly interacting with the receptor's ion channel. By activation with UV light it can be made to react covalently with its binding site in the receptor protein. Here a method is described to perform this photolabeling with a time resolution comparable to the physiological event of channel opening and closing. By this technique structural transitions within the receptor can be visualized and transient conformational states can be labeled covalently and irreversibly.     

Additive partitioning of aquatic invertebrate species diversity across multiple spatial scales

1. Additive partitioning of three measures of diversity (species richness, Shannon's diversity index H and Simpson's diversity D) was used to study the relationship between local and regional diversity of benthic macroinvertebrate communities of boreal lakes (littoral habitats) and streams (riffle habitats) across three spatial scales (sampling sites, ecoregions and biogeographic regions). 2. Alpha (α) and beta (β) diversity are defined as within‐habitat and between‐habitat diversity, respectively. According to the concept of additive partitioning, diversity can be partitioned across multiple spatial scales such that the total (γ) diversity on one spatial scale becomes within‐habitat (α) diversity at the next higher scale. Hence, the total diversity at one scale is determined by the α diversity and the between‐habitat diversity (β) at the next lower scale. Consequently, one of the advantages of additive partitioning is that it is possible to study simultaneously β diversity and the regional‐local species relationship and the scale dependence of α and β components. 3. For both lakes and streams α diversity was low for sites and ecoregions, whereas β diversity was high, indicating that among‐site factors are important in describing the variability among the lakes and streams studied here. 4. Weak, albeit significant, evidence was found for regional and local species saturation patterns. Multiple stepwise regression indicated that local processes might be more important in structuring lake‐littoral and stream‐riffle species assemblages than regional processes. From these results we conclude that environmental heterogeneity may act as an important factor contributing to species coexistence, resulting in the observed saturation patterns. 5. Our study supports the use of additive partitioning for identifying specific patterns of macroinvertebrate diversity on multiple spatial scales and the underlying processes generating these patterns. This information is needed to improve understanding of the relation between patterns and processes affecting (decreasing) trends in aquatic biodiversity.     

黄河下游平原非农植物多样性拆分研究

非农生物多样性的存在是农业景观生态系统健康持续发展的基础,对农业景观非农生境中植物群落物种多样性特征分析将有助于可持续农业景观构建措施的科学提出。在黄河下游平原典型农业景观中采用栅格分区的方式布设样点(共54个),采用典型样地法对各样点内的林地、树篱、田间道路和沟渠等主要非农生境的植物群落进行调查,采用生物多样性加性分配的方法探讨不同空间尺度上生物多样性的组成特征。结果显示:(1)各非农生境间植物群落物种多样性特征存在较大的差异。(2)偶见种从数量上构成了各非农生境中植物物种丰富度的主体,而常见种则行使着群落优势种和构建者的角色。(3)总体上,β多样性在各空间尺度中均对总物种丰富度具有重要贡献。(4)常见种和偶见种中物种组成格局存在显著差异:常见种的物种丰富度主要由α多样性贡献,而β多样性则贡献了偶见种的绝大部分。简言之,β多样性对区内植物多样性的保护和维持意义重大,农业景观中非农生境类别的出现对总物种丰富度的提高具有重要作用;各生境中较高的样点间β多样性(β样点)意味着在看似均质化的农业景观背景中依然具有较高的区域差异;景观组成和构型的变化将对农业景观中植物群落特征和物种多样性产生重要影响,且对偶见种的影响更甚。未来,应从景观和区域等更大尺度上,基于农业景观生态系统功能和服务的综合考虑及可持续农业景观的建立来探讨农业活动与生物多样性保护的权衡。     

Additive diversity partitioning as a guide to regional montane reserve design in Asia: an example from Yunnan Province,China

Aim Data on spatial and temporal turnover in species composition within a region is essential to design regional protected areas. Montane systems are often recognized as biodiversity hotspots. The primary objective of this study is to identify patterns of montane bird diversity across multiple spatial and temporal scales using an additive diversity partitioning framework. Location The Ailao Mountains, central Yunnan Province, China. Methods We used point counts to sample bird communities in four elevational zones, on eastern and western slopes, during both the breeding and the non‐breeding seasons. Diversity (richness and Shannon) was partitioned across space (points, elevational zones and slopes) and time (seasons). We used permutation tests to compare observed values to values expected by random chance. A complementary cluster analysis was also used to evaluate beta diversity. Results Overall, the gamma diversity was attributed to significantly higher beta diversity (relative to that of randomization tests) among elevational zones and, to a lesser extent, between slopes. For Shannon–Wiener Index, beta diversity between seasons was significantly higher than expected and had a similar contribution to the gamma diversity as with beta diversity between slopes. Hierarchical cluster analysis supported the findings for Shannon–Wiener Index. The contribution of beta diversity among points to gamma diversity within each elevational zone generally lessened with increasing elevation. Main conclusions Our results show significantly high levels of beta diversity among elevational zones and between slopes, as well as between seasons for Shannon diversity, in a small area of the Ailao Mountain range. Thus, a regional montane reserve system should cover the entire elevational gradient and multiple slopes, rather than only the montane crest. Furthermore, higher pattern diversity in lower elevational zones suggests that larger areas should be preserved at lower elevational zones. Finally, the design of regional reserve systems require more studies conducted at multiple seasons at a regional scale.     

Alloxan-induced luminol luminescence as a tool for investigating mechanisms of radical-mediated diabetogenicity.

It is not clear whether the muscle wasting commonly observed in hyperthyroidism is due to alteration in the rate of protein synthesis or degradation. The effect of experimental hyperthyroidism on skeletal-muscle proteolysis in the rat was studied by measuring alanine and tyrosine release from isolated skeletal muscles in vitro and 3-methyl-histidine excretion in vivo. Alanine release from the isolated epitrochlaris-muscle preparation was increased as soon as 24h after a 25 microgram dose of L-tri-iodothyronine in vivo. Conversely, alanine release from muscles of hypothyroid rats was decreased, but restored by L-tri-iodothyronine supplementation before death. Furthermore, 3-methylhistidine excretion was increased in hyperthyroid rats throughout an 18-day treatment period. The increased amino acid release from isolated muscles and the increased 3-methylhistidine excretion in vivo strongly suggests that hyperthyroidism increases skeletal-muscle proteolysis. Furthermore, the thyroid-hormone concentration may be an important factor in regulating muscle proteolysis.     

Functional magnetic resonance imaging as a tool for investigating human cortical motor function.

Non-invasive functional magnetic resonance imaging (fMRI) mapping techniques sensitive to the local changes of blood flow, blood volume, and blood oxygenation which accompany neuronal activation have been widely used over the last few years to investigate the functional organization of human cortical motor systems, and specifically of the primary motor cortex. Validation studies have demonstrated a good correspondence between quantitative and topographic aspects of data acquired by fMRI and positron emission tomography. The spatial and temporal resolution affordable by fMRI has allowed to achieve new important information on the distributed representation of hand movements in multiple functional modules, and on the intensity and spatial extent of neural activation in the contralateral and ipsilateral primary motor cortex in relation to parametric and nonparametric aspects of movement and to the degree of handedness. Neural populations with different functional characteristics have been identified in anatomically defined regions, and the temporal aspects of the activation during voluntary movement tracked in different components of the motor system. Finally, this technique has proved useful to deepen our understanding of the neural basis of motor imagery, demonstrating increased activity in the primary motor cortex during mental representation of sequential finger movements.