Correction to: Exposing the hidden half: root research at the forefront of science

Plant and Soil - In the published version of this editorial paper, the sentence in the first paragraph should be corrected as shown below.     

Exposing hidden endemism in a Neotropical forest raptor using citizen science

Gaps in our knowledge of the geographical distribution of species represent a fundamental challenge to biogeographers and conservation biologists alike, and are particularly pervasive in the tropics. Here we highlight the case of the Rufous‐thighed Kite Harpagus diodon, a South American raptor commonly mapped as resident across half the continent. Recent observations at migration watch points have indicated it may be partially migratory in the southernmost parts of its range. To investigate this possibility, we collated contemporary and historical specimen records, published sight records and ‘digital vouchers’ – photographs and sound‐recordings archived online (from citizen science initiatives) – and explored the spatiotemporal distribution of records. We were unable to trace any documented records of this species from Amazonia during the austral summer (October–March), or records from the Atlantic Forest biome during the peak of the Austral winter (June–August), and all proven breeding records stem from the Atlantic Forest region. We compared this pattern with that of a ‘control’ species, the congeneric Double‐toothed Kite H. bidentatus, again using specimens and digital vouchers. For this species we found no evidence of seasonality between biomes and can disregard spatiotemporal variation in observer effort as a cause of seasonal biases. We consider that all populations of Rufous‐thighed Kites are fully migratory, wintering in Equatorial forests in the Amazonian basin. We provide evidence that this pattern was previously obscured by erroneous undocumented records and poor or erroneous specimen metadata, and its discovery was primarily facilitated by digital vouchers. This discovery requires a reassessment of the species’ global conservation status as an Atlantic Forest breeding endemic, threatened by habitat loss and degradation, as it was previously considered to be resident across large swathes of undisturbed Amazonian Forest on the Guiana Shield. The bulk of the digital voucher data used to elucidate this pattern were extracted from a Brazilian citizen science initiative WikiAves, which may serve as a model for collating biodiversity data in megadiverse countries and help catalyse environmental awareness.     

Uncovering the hidden half of plants using new advances in root phenotyping

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Exposing a hidden functional site of C-reactive protein by site-directed mutagenesis

C-reactive protein (CRP) is a cyclic pentameric protein whose major binding specificity, at physiological pH, is for substances bearing exposed phosphocholine moieties. Another pentameric form of CRP, which exists at acidic pH, displays binding activity for oxidized LDL (ox-LDL). The ox-LDL-binding site in CRP, which is hidden at physiological pH, is exposed by acidic pH-induced structural changes in pentameric CRP. The aim of this study was to expose the hidden ox-LDL-binding site of CRP by site-directed mutagenesis and to generate a CRP mutant that can bind to ox-LDL without the requirement of acidic pH. Mutation of Glu(42), an amino acid that participates in intersubunit interactions in the CRP pentamer and is buried, to Gln resulted in a CRP mutant (E42Q) that showed significant binding activity for ox-LDL at physiological pH. For maximal binding to ox-LDL, E42Q CRP required a pH much less acidic than that required by wild-type CRP. At any given pH, E42Q CRP was more efficient than wild-type CRP in binding to ox-LDL. Like wild-type CRP, E42Q CRP remained pentameric at acidic pH. Also, E42Q CRP was more efficient than wild-type CRP in binding to several other deposited, conformationally altered proteins. The E42Q CRP mutant provides a tool to investigate the functions of CRP in defined animal models of inflammatory diseases including atherosclerosis because wild-type CRP requires acidic pH to bind to deposited, conformationally altered proteins, including ox-LDL, and available animal models may not have sufficient acidosis or other possible modifiers of the pentameric structure of CRP at the sites of inflammation.     

AACR Annual Meeting 2008: autophagy in the forefront of cancer research

The 2008 American Association for Cancer Research (AACR) Annual Meeting was held in San Diego, CA, April 12-16, 2008 (http:// www.aacr.org/home/scientists/meetings--workshops/annual-meeting-2008.aspx). More than 17,000 scientists from 60 countries participated in this meeting that was organized by AACR, the oldest and largest organization in the world focused on cancer research. The scientific presentations included more than 6,000 abstracts and 500 invited talks on new and significant discoveries in basic, clinical, and translational cancer research. Autophagy, as pertaining to tumorigenesis and response to anticancer therapies, was undoubtedly a "hot topic" in this meeting. An educational session, a forum, a minisymposium and several other talks dispersed in different sessions had a strong focus on autophagy. All autophagy-related presentations were very well attended and stimulated lively discussions, clearly indicating that the scientific community is greatly interested in this rapidly-progressing area of research.     

Cyclic dinucleotides at the forefront of innate immunity

Cyclic dinucleotides (CDNs) have emerged as ubiquitous signaling molecules in all domains of life. In eukaryotes, CDN signaling systems are evolutionarily ancient and have developed to sense and respond to pathogen infection. On the other hand, dysregulation of these pathways has been implicated in the pathogenesis of autoimmune diseases. Thus, CDNs have garnered major interest over recent years for their ability to elicit potent immune responses in the eukaryotic host. Similarly, ancestral CDN-based signaling systems also appear to confer immunological protection against infection in prokaryotes. Therefore, a better understanding of the host processes regulated by CDNs will be of tremendous value in many areas of research. Here, we aim to review the latest discoveries and recent trends in CDN research with a particular focus on the molecular mechanisms by which these small molecules mediate innate immunity.     

Hemiascomycetous yeasts at the forefront of comparative genomics

With more than a dozen species fully sequenced, as many as this partially sequenced, and more in development, yeasts are now used to explore the frontlines of comparative genomics of eukaryotes. Innovative procedures have been developed to compare and annotate genomes at various evolutionary distances, to identify short cis-acting regulatory elements, to map duplications, or to align syntenic blocks. Human and plant pathogens, in addition to yeasts that show a variety of interesting physiological properties, are included in this multidimensional comparative survey, which encompasses a very broad evolutionary range. As major steps of the evolutionary history of hemiascomycetous genomes emerge, precise questions on the general mechanisms of their evolution can be addressed, using both experimental and in silico methods.     

Ubiquitination of transporters at the forefront of plant nutrition

In plants, the tight regulation of plasma membrane transporters is essential to maintain nutrient homeostasis. The mechanisms controlling the abundance of transporters, and other integral plasma membrane proteins, now come to light. Ubiquitination appears as a major signal initiating cargo endocytosis and sorting into multivesicular bodies prior to degradation in the vacuole. We have indeed demonstrated that the root iron transporter IRT1 is subjected to ubiquitin-dependent trafficking in root epidermal cells. This control is crucial to keep IRT1 levels at the cell surface low and to cope with the toxicity associated with other readily available metal substrates of IRT1. Our work combined with recent report on the BOR1 boron transporter establishes ubiquitination as a conserved mechanism of plasma membrane protein trafficking in plants and highlights its importance for plant nutrition.Key words: Endocytosis, Iron, IRT1, BOR1, Degradation, monoubiquitinPlasma membrane transporters play a pivotal role in all living organisms by providing the cell surface with a selective barrier for a wide range of nutrients, small molecules and ions. These transport proteins are very often under the control of sophisticated molecular mechanisms to adapt to changing environmental conditions and to ensure optimal absorption of their cognate substrates. Although the molecular events controlling the abundance of plasma membrane proteins at the cell surface are largely documented in non-plant model organisms, the situation in plants is much less understood. This is particularly true for the well-established ubiquitin-dependent endocytosis and sorting in late endosomes of plasma membrane proteins, for which evidence is still lacking in plants.Recently, we showed that the root iron transporter IRT1 from the model plant Arabidopsis thaliana, which mediates Fe²⁺ and other divalent metal absorption from the soil,¹ surprisingly localizes to the early endosomes/trans-Golgi network compartment (EE/TGN).² Pharmacological interference with vesicular trafficking highlighted the dynamic behavior of IRT1 in root epidermal cells. IRT1, although localized to EE/TGN, rapidly cycles to the plasma membrane to perform iron uptake from the soil. We demonstrated that IRT1 is ubiquitinated in vivo and carries monoubiquitin moieties on several cytosol-exposed lysine residues, a process known as multiubiquitination. Reminiscent of the ubiquitin-dependent endocytosis and degradation of animal receptor tyrosine kinases and yeast nutrient permeases,^3,4 we hypothesized that IRT1 ubiquitination may control its dynamics in the cell. Transgenic plants expressing a mutant version of IRT1 in which two lysine residues were replaced by arginine (IRT1_K154K179R) indeed show accumulation of IRT1 protein at the plasma membrane. This clearly establishes the role of ubiquitination in driving IRT1 intracellular trafficking.Whether the cell surface localization of IRT1_K154K179R reflects a role of ubiquitination in the internalization from the plasma membrane, in the sorting at the multivesicular bodies, or both is an open question. Interestingly, IRT1_K154K179R-expressing plants displayed dramatic growth reduction, likely due to uncontrolled uptake of metals. Altogether, our work demonstrates the existence of monoubiquitin-dependent endocytosis in plants and reveals its crucial role in keeping IRT1 level at the plasma membrane low to prevent metal toxicity. The uptake of Fe²⁺ by IRT1 indeed requires the prior reduction of Fe³⁺ by the FRO2 ferric chelate reductase, whose activity was shown to be limiting for iron uptake.^5–7 The amount of Fe²⁺ produced by FRO2 is therefore low and favors the uptake of other substrates of IRT1 such as Zn²⁺, Mn²⁺, Co²⁺ and Cd²⁺. Limiting the pool of IRT1 at the plasma membrane by ubiquitin-dependent endocytosis appears as a protective mechanism to limit the absorption of readily available metals other than iron. This also highlights the necessity for a strict co-regulation of FRO2 and IRT1 to optimize iron uptake. The overexpression of IRT1 in transgenic Arabidopsis plants consequently leads to a strong overload of Zn and Mn in roots and aerial tissues, while iron only very mildly accumulates. This, combined with the existence of point mutants of IRT1 with altered selectivity,⁸ offers the long term perspective of engineering transgenic plants designed to phytoremediate polluted soil for a given element.Only a handful of plasma membrane proteins were shown to be ubiquitinated in plants, including the PIN2 auxin efflux carrier,⁹ the FLS2 flagellin receptor¹⁰ and the PIP2;1 water channel.¹¹ Yet, the role of ubiquitination for such proteins remained unclear until very recently. Along with our recent report of monoubiquitin-dependent trafficking of IRT1 came a similar study on the Arabidopsis BOR1 boron transporter. Like iron, boron is essential for plants but toxic when present in excess. BOR1 has been previously shown to be regulated by boron-inducible endocytosis and degradation in the vacuole.¹² Kasai et al.¹³ now showed that high boron concentrations induced BOR1 mono- or diubiquitination and that mutation of a single lysine residue affected BOR1 trafficking to the vacuole.¹³ In yeast and mammals, ubiquitination has been shown to trigger the internalization of plasma membrane proteins from the cell surface and sorting in multivesicular bodies/late endosomes (MVBs/LEs) for targeting and degradation in the vacuole/lysosomes,^3,4 although recent reports emphasize the role of ubiquitination in later stages of endocytosis.¹⁴ Similarly, BOR1 ubiquitination is not required for endocytosis from the plasma membrane, this step being probably mediated by tyrosine-based motives found on its cytosolic face,¹⁵ but is crucial for the sorting of BOR1 in multivesicular bodies for subsequent targeting and degradation in the vacuole.¹³It will be interesting to pinpoint the exact role of IRT1 ubiquitination in either the control of its internalization from the plasma membrane, the targeting to the internal vesicles of multivesicular bodies for delivery to the vacuole, or both. Hence, ubiquitination constitutes a conserved process controlling the localization and the fate of plasma membrane proteins, and appears as a critical mechanism to maintain iron and boron homeostasis in plants (Fig. 1). The quest for the machinery driving the ubiquitination of plasma membrane proteins has now begun. Already, the PUB12 and PUB13 U-box E3 ubiquitin ligases have just been reported to polyubiquitinate the FLS2 flagellin receptor, driving its flagellin-dependent degradation and preventing excessive or prolonged activation of immune responses.¹⁶ Whether these E3 ubiquitin ligases, or members from the same family, act on other plasma membrane proteins will have to be determined in the future. This will provide breakthrough information on how the dynamics and the fate of integral plasma membrane proteins are driven, and will highlight the importance of ubiquitination in important biological processes such as nutrition, response to pathogens and hormone transport.Open in a separate windowFigure 1Ubiquitin-dependent trafficking of plasma membrane proteins in plants. Diagram illustrating the role of ubiquitination throughout the endocytic pathway of plant plasma membrane proteins with the example of IRT 1 (in orange) and BOR1 (in blue). IRT 1 multiubiquitination (red circles) controls either its internalization from the plasma membrane and/or its sorting in late endosomes required for vacuolar targeting, to maintain IRT 1 low at the plasma membrane independently of iron nutrition. BOR1 mono- or diubiquitination (yellow circle) is required when plants are exposed to high boron for BOR1 sorting in multivesicular bodies and subsequent targeting to the vacuole for degradation. The interplay of ubiquitin ligases and deubiquitinases thereby controls the dynamics of plasma membrane proteins. PM, plasma membrane; EE /TGN, Early endosome/Trans-Golgi network; MVB/LE , Multivesicular body/Late endosome compartment; B, Boron; M²⁺, Metals transported by IRT 1 in addition to Fe²⁺.     

A glimpse of life science research at Tsinghua

<正>Life Science at Tsinghua University has a long and eventful history.The Biology Department,founded in 1926,was among the oldest and most prestigious in China.In 1952,the Biology Department,together with other natural science departments,were eliminated from the University by order of the central government.In 1984,the Department of Biological Science and Biotechnology was re-established,with Professor Poo Mu-ming being the founding Director.In the ensuing 25 years,the Department went through rapid transformations and gained national and international recognition.In September 2009,the Department of Biological Science and Biotechnology was replaced by the School of Life Sciences.     

神经科学：脑研究的综合学科

目录一、神经科学对社会和科学发展的意义（一）神经科学对社会健康的意义（二）神经科学对社会发展的意义（三）神经科学发展的科学意义（四）国际社会和国际科技界对神经科学的重视二、神经科学前沿简介（一）脑的高级功能（二）脑和神经系统的疾病（三）脑发育的分子原...     

European Christians are at the forefront in accepting evolution: results from an internet-based survey

Beliefs regarding the origins of the universe and life differ substantially between groups of people and are often particularly associated with religious worldviews. It is important to understand factors associated with evolution and creationism beliefs and unacceptance of scientific evidence for evolution. An internet-based survey was conducted to elicit information from people who self-identify as Christians, atheists, agnostics and other belief systems, as well as by geographical location and other demographic variables, on acceptance of evolution or creationism, certainty with which each position is believed, and reasons for rejecting the alternative. It was found that almost 60% of Christians believe in creationism and less than 10% believe in natural evolution. Worldwide, these proportions were relatively consistent across all locations except for in Europe. Among European Christians the majority of Christians believe in a form of evolution. It was found that the vast majority (87%) of Christians are 'absolutely certain' about their beliefs, compared with the minority of atheists and agnostics claiming 'absolute certainty'. Generally, reasons Christians did not accept evolution were based not on evidence but on religious doctrine. In contrast, the most common reason for not accepting the existence of a god by atheists who supported evolution was the lack of evidence. Innovative strategies may be required to communicate evolutionary science effectively to non-European Christians.     

Ectomycorrhiza of Kobresia myosuroides at a primary successional glacier forefront

The bog sedge Kobresia myosuroides is among the first ectomycorrhizal (EM) plants forming dense pads on receding glacier forefronts of the Austrian Alps. This is the only Cyperaceae species known to form EM. To date, little is known about fungal species involved in these EM associations. Therefore, the main aim of this study was to detect EM fungal communities of K. myosuroides (1) by describing mycorrhizal morphotypes (MT) and (2) by identifying the mycobionts by rDNA internal transcribed spacer (ITS) sequencing. Furthermore, seasonal dynamics of Kobresia mycobionts were investigated. Sampling was performed in all four seasons (also under snow cover) during the years 2005 and 2006 at the Rotmoos glacier forefront, a well-characterized alpine primary successional habitat in the Austrian alps (2,300 m above sea level). The degree of EM infection of K. myosuroides roots was high (95%). Ten MTs were described and sequences of 18 fungal taxa were obtained. This was the highest mycobiont diversity ever reported for this plant. Cenococcum geophilum was the most abundant mycobiont (37-46%) and shared dominancy with Sebacina incrustans (16-44%) and Tomentella spp. (7-37%). Tomentella (including Thelephora) was the most species-rich mycobiont genus with five taxa, followed by Cortinarius, Inocybe, and Sebacina with two taxa each and one Hebeloma species. Other ascomycete mycobionts beside C. geophilum were Helvella sp., Lecythophora sp., and one Pezizales species. Due to high interannual differences in the EM fungal community, no significant seasonal changes could be detected. The importance of fungal mycobionts in alpine habitats is discussed.