Increasing extent of periods of no flow in intermittent waterways promotes heterotrophy

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The cell biology of lignification in higher plants

Background Lignin is a polyphenolic polymer that strengthens and waterproofs the cell wall of specialized plant cell types. Lignification is part of the normal differentiation programme and functioning of specific cell types, but can also be triggered as a response to various biotic and abiotic stresses in cells that would not otherwise be lignifying.Scope Cell wall lignification exhibits specific characteristics depending on the cell type being considered. These characteristics include the timing of lignification during cell differentiation, the palette of associated enzymes and substrates, the sub-cellular deposition sites, the monomeric composition and the cellular autonomy for lignin monomer production. This review provides an overview of the current understanding of lignin biosynthesis and polymerization at the cell biology level.Conclusions The lignification process ranges from full autonomy to complete co-operation depending on the cell type. The different roles of lignin for the function of each specific plant cell type are clearly illustrated by the multiple phenotypic defects exhibited by knock-out mutants in lignin synthesis, which may explain why no general mechanism for lignification has yet been defined. The range of phenotypic effects observed include altered xylem sap transport, loss of mechanical support, reduced seed protection and dispersion, and/or increased pest and disease susceptibility.     

冻融作用对陆地生态系统氮循环关键过程的影响效应及其机制

冻融作用是中、高纬度及高海拔地区土壤普遍存在的一种自然现象,是非生长季陆地生态系统氮循环的重要影响因素.冻融作用主要通过改变土壤的理化性质及生物学性状来影响氮素在土壤中的迁移与转化.目前,冻融作用对陆地生态系统氮循环各个过程影响的研究结果不尽一致,理论机制尚不明晰,研究方法也需进一步地探索与创新,因此有必要对现有成果进行梳理和分析,以更好地把握冻融作用下的氮循环过程.本文结合国内外已有研究成果,论述了冻融作用对陆地生态系统氮循环关键过程（氮矿化、固持、硝化与反硝化过程、氮淋溶及气态损失）的影响效应及其主要机制,对目前研究中存在的不足进行了剖析,并对未来研究中迫切需要关注的重点研究方向进行了探讨与展望.     

Parallel declines in survival of adult Northern Fulmars Fulmarus glacialis at colonies in Scotland and Ireland

Assessing broad‐scale changes in seabird populations across the North Atlantic requires an integration of available datasets to understand the spatial extent of potential drivers and demographic change. Here, we compared survival of Northern Fulmars Fulmarus glacialis from a Scottish and an Irish colony from 1974 to 2009. Despite lower recapture probabilities of monel‐ringed Irish birds compared with colour‐ringed Scottish birds, survival probability decreased at both colonies. The extent to which the decline in survival is related to density‐dependent processes or other external drivers remains uncertain, but our results suggest that these changes in survival are possibly indicative of larger‐scale processes and are not confined to local colony dynamics.     

Commentary: When does understanding phenotypic evolution require identification of the underlying genes?

Adaptive evolution is fundamentally a genetic process. Over the past three decades, characterizing the genes underlying adaptive phenotypic change has revealed many important aspects of evolutionary change. At the same time, natural selection is often fundamentally an ecological process that can often be studied without identifying the genes underlying the variation on which it acts. This duality has given rise to disagreement about whether, and under what circumstances, it is necessary to identify specific genes associated with phenotypic change. This issue is of practical concern, especially for researchers who study nonmodel organisms, because of the often enormous cost and labor required to “go for the genes.” We here consider a number of situations and questions commonly addressed by researchers. Our conclusion is that although gene identification can be crucial for answering some questions, there are others for which definitive answers can be obtained without finding underlying genes. It should thus not be assumed that considerations of “empirical completeness” dictate that gene identification is always desirable.     

Variability in nitrogen stable isotope ratios of macroalgae: consequences for the identification of nitrogen sources

In our research, we collected and analyzed numerous macroalgal specimens (738) for isotopic analysis sampled over a year at monthly intervals across 20 sites within the Urías lagoon complex, a typical subtropical coastal ecosystem located in the Gulf of California. We quantified and characterized (chemically and isotopically) the N loads received by Urías throughout a year. We studied the spatial‐temporal variation of the chemical forms and isotopic signals of the available N in the water column, and we monitored in situ different environmental variables and other hydrodynamic parameters. Multiple N sources (e.g., atmospheric, sewage, seafood processing, agriculture and aquaculture effluents) and biogeochemical reactions related to the N cycle (e.g., ammonia volatilization, nitrification and denitrification) co‐occurring across the ecosystem, result in a mixture of chemical species and isotopic compositions of available N in the water column. Increased variability was observed in the δ¹⁵N values of macroalgae (0.41‰–22.67‰). Based on our results, the variation in δ¹⁵N was best explained by spatio‐temporal changes in available N and not necessarily related to the N sources. The variability was also explained by the differences in macroalgal biology among functional groups, species and/or individuals. Although the δ¹⁵N‐macroalgae technique was a useful tool to identify N sources, its application in coastal ecosystems receiving multiple N sources, with changing environmental conditions influencing biogeochemical processes, and high diversity of ephemeral macroalgal species, could be less sensitive and have less predictive power.     

Design and performance of combined infrared canopy and belowground warming in the B4WarmED (Boreal Forest Warming at an Ecotone in Danger) experiment

Conducting manipulative climate change experiments in complex vegetation is challenging, given considerable temporal and spatial heterogeneity. One specific challenge involves warming of both plants and soils to depth. We describe the design and performance of an open‐air warming experiment called Boreal Forest Warming at an Ecotone in Danger (B4WarmED) that addresses the potential for projected climate warming to alter tree function, species composition, and ecosystem processes at the boreal‐temperate ecotone. The experiment includes two forested sites in northern Minnesota, USA, with plots in both open (recently clear‐cut) and closed canopy habitats, where seedlings of 11 tree species were planted into native ground vegetation. Treatments include three target levels of plant canopy and soil warming (ambient, +1.7 °C, +3.4 °C). Warming was achieved by independent feedback control of voltage input to aboveground infrared heaters and belowground buried resistance heating cables in each of 72‐7.0 m² plots. The treatments emulated patterns of observed diurnal, seasonal, and annual temperatures but with superimposed warming. For the 2009 to 2011 field seasons, we achieved temperature elevations near our targets with growing season overall mean differences (?T_below) of +1.84 °C and +3.66 °C at 10 cm soil depth and (?T^above) of +1.82 °C and +3.45 °C for the plant canopies. We also achieved measured soil warming to at least 1 m depth. Aboveground treatment stability and control were better during nighttime than daytime and in closed vs. open canopy sites in part due to calmer conditions. Heating efficacy in open canopy areas was reduced with increasing canopy complexity and size. Results of this study suggest the warming approach is scalable: it should work well in small‐statured vegetation such as grasslands, desert, agricultural crops, and tree saplings (<5 m tall).     

The formation of species pools: historical habitat abundance affects current local diversity

Aim Explanations of biogeographic diversity patterns have emphasized the role of large‐scale processes that determine species pools, whereas explanations of local patterns have not. We address the hypothesis that local diversity patterns are also primarily dependent on the size of the available species pools, which are expected to be large when the particular habitat type has been evolutionary more abundant, or in unproductive habitats due to shorter generation time and hence higher diversification rates. Location The Canary Islands. Methods We determined the geographic distribution and habitat requirements of all native vascular plant species in the Canary Islands. Species pools for each habitat type on particular islands were further split into two categories according to origin: either originating due to local diversification or due to natural immigration. The dependence of historical diversification and diversification rate on habitat type, area, age, altitude and distance to the mainland was tested with general linear mixed models weighed according to the Akaike information criterion. Results The largest portion of the local variation in plant species diversity was attributed to the historic (pre‐human) habitat area, although island age was also important. The diversification rate was higher in unproductive habitats of coastal scrub and summit vegetation. Main conclusion Our study supports the species pool hypothesis, demonstrating that natural local patterns of species diversity in different habitats mirror the abundance of those particular habitats in evolutionary history. It also supports the community‐level birth rate hypothesis, claiming that stressful conditions result in higher diversification rates. We conclude that much of the observed local variation in plant diversity can be attributed to the differing sizes of species pools evolved under particular habitat conditions, and that historic parameters are far more important determinants of local diversity than suggested by ecological theory.     

Characterizing the normal proteome of human ciliary body

Background

The ciliary body is the circumferential muscular tissue located just behind the iris in the anterior chamber of the eye. It plays a pivotal role in the production of aqueous humor, maintenance of the lens zonules and accommodation by changing the shape of the crystalline lens. The ciliary body is the major target of drugs against glaucoma as its inhibition leads to a drop in intraocular pressure. A molecular study of the ciliary body could provide a better understanding about the pathophysiological processes that occur in glaucoma. Thus far, no large-scale proteomic investigation has been reported for the human ciliary body.

Results

In this study, we have carried out an in-depth LC-MS/MS-based proteomic analysis of normal human ciliary body and have identified 2,815 proteins. We identified a number of proteins that were previously not described in the ciliary body including importin 5 (IPO5), atlastin-2 (ATL2), B-cell receptor associated protein 29 (BCAP29), basigin (BSG), calpain-1 (CAPN1), copine 6 (CPNE6), fibulin 1 (FBLN1) and galectin 1 (LGALS1). We compared the plasma proteome with the ciliary body proteome and found that the large majority of proteins in the ciliary body were also detectable in the plasma while 896 proteins were unique to the ciliary body. We also classified proteins using pathway enrichment analysis and found most of proteins associated with ubiquitin pathway, EIF2 signaling, glycolysis and gluconeogenesis.

Conclusions

More than 95% of the identified proteins have not been previously described in the ciliary body proteome. This is the largest catalogue of proteins reported thus far in the ciliary body that should provide new insights into our understanding of the factors involved in maintaining the secretion of aqueous humor. The identification of these proteins will aid in understanding various eye diseases of the anterior segment such as glaucoma and presbyopia.