Modelling temperature-driven changes in species associations across freshwater communities

Due to global climate change–induced shifts in species distributions, estimating changes in community composition through the use of Species Distribution Models has become a key management tool. Being able to determine how species associations change along environmental gradients is likely to be pivotal in exploring the magnitude of future changes in species’ distributions. This is particularly important in connectivity-limited ecosystems, such as freshwater ecosystems, where increased human translocation is creating species associations over previously unseen environmental gradients. Here, we use a large-scale presence–absence dataset of freshwater fish from lakes across the Fennoscandian region in a Joint Species Distribution Model, to measure the effect of temperature on species associations. We identified a trend of negative associations between species tolerant of cold waters and those tolerant of warmer waters, as well as positive associations between several more warm-tolerant species, with these associations often shifting depending on local temperatures. Our results confirm that freshwater ecosystems can expect to see a large-scale shift towards communities dominated by more warm-tolerant species. While there remains much work to be done to predict exactly where and when local extinctions may take place, the model implemented provides a starting-point for the exploration of climate-driven community trends. This approach is especially informative in regards to determining which species associations are most central in shaping future community composition, and which areas are most vulnerable to local extinctions.     

Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes

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Olfactomedin-1 Has a V-shaped Disulfide-linked Tetrameric Structure

Olfactomedin-1 (Olfm1; also known as noelin and pancortin) is a member of the olfactomedin domain-containing superfamily and a highly expressed neuronal glycoprotein important for nervous system development. It binds a number of secreted proteins and cell surface-bound receptors to induce cell signaling processes. Using a combined approach of x-ray crystallography, solution scattering, analytical ultracentrifugation, and electron microscopy we determined that full-length Olfm1 forms disulfide-linked tetramers with a distinctive V-shaped architecture. The base of the “V” is formed by two disulfide-linked dimeric N-terminal domains. Each of the two V legs consists of a parallel dimeric disulfide-linked coiled coil with a C-terminal β-propeller dimer at the tips. This agrees with our crystal structure of a C-terminal coiled-coil segment and β-propeller combination (Olfm1^coil-Olf) that reveals a disulfide-linked dimeric arrangement with the β-propeller top faces in an outward exposed orientation. Similar to its family member myocilin, Olfm1 is stabilized by calcium. The dimer-of-dimers architecture suggests a role for Olfm1 in clustering receptors to regulate signaling and sheds light on the conformation of several other olfactomedin domain family members.     

Nucleic acid oxidation: an early feature of Alzheimer's disease

Studies of oxidative damage during the progression of Alzheimer's disease (AD) suggest its central role in disease pathogenesis. To investigate levels of nucleic acid oxidation in both early and late stages of AD, levels of multiple base adducts were quantified in nuclear and mitochondrial DNA from the superior and middle temporal gyri (SMTG), inferior parietal lobule (IPL), and cerebellum (CER) of age‐matched normal control subjects, subjects with mild cognitive impairment, preclinical AD, late‐stage AD, and non‐AD neurological disorders (diseased control; DC) using gas chromatography/mass spectrometry. Median levels of multiple DNA adducts in nuclear and mitochondrial DNA were significantly (p ≤ 0.05) elevated in the SMTG, IPL, and CER in multiple stages of AD and in DC subjects. Elevated levels of fapyguanine and fapyadenine in mitochondrial DNA suggest a hypoxic environment early in the progression of AD and in DC subjects. Overall, these data suggest that oxidative damage is an early event not only in the pathogenesis of AD but is also present in neurodegenerative diseases in general.

     

Should a standing or seated reference posture be used when normalizing seated spine kinematics?

Currently in the literature there is no consensus on which procedure for normalizing seated spine kinematics is most effective. The objective of this study was to examine the changes in the range of motion (ROM) of seated posture trials when expressed as a percent of maximum standing and seated ROM. A secondary purpose was to determine whether the typical maximum planar calibration movements (flexion, lateral-bend, and axial twist) elicited the respective maximum ROM values for each spine region versus postures with specific movement instruction. Thirteen male participants completed seven different movement trials. These consisted of the maximum planar movement trials, with the remaining four postures being combinations of specific lumbar and thoracic movements. Global and relative angles for the upper-thoracic, mid-thoracic, lower-thoracic, and lumbar regions were calculated and normalized to both a seated and standing reference posture. When normalizing both global and relative angles the standing reference appears optimal for flexion, twisting and lateral bend angles in all spine regions, with the exception of relative flexion angle in the mid-thoracic region. The maximum planar movement trials captured the greatest ROM for each global angle, relative lower-thoracic angle and relative lumbar flexion angle, but did not for all other relative angles in the upper-thoracic, mid-thoracic, and lumbar regions. If future researchers can only collect one reference posture these results recommend that a standing reference posture be collected for normalizing seated spine kinematics, although a seated reference posture should be collected if examining relative flexion angles at the mid-thoracic region.     

Fungal Endopolygalacturonases Are Recognized as Microbe-Associated Molecular Patterns by the Arabidopsis Receptor-Like Protein RESPONSIVENESS TO BOTRYTIS POLYGALACTURONASES1

Plants perceive microbial invaders using pattern recognition receptors that recognize microbe-associated molecular patterns. In this study, we identified RESPONSIVENESS TO BOTRYTIS POLYGALACTURONASES1 (RBPG1), an Arabidopsis (Arabidopsis thaliana) leucine-rich repeat receptor-like protein, AtRLP42, that recognizes fungal endopolygalacturonases (PGs) and acts as a novel microbe-associated molecular pattern receptor. RBPG1 recognizes several PGs from the plant pathogen Botrytis cinerea as well as one from the saprotroph Aspergillus niger. Infiltration of B. cinerea PGs into Arabidopsis accession Columbia induced a necrotic response, whereas accession Brno (Br-0) showed no symptoms. A map-based cloning strategy, combined with comparative and functional genomics, led to the identification of the Columbia RBPG1 gene and showed that this gene is essential for the responsiveness of Arabidopsis to the PGs. Transformation of RBPG1 into accession Br-0 resulted in a gain of PG responsiveness. Transgenic Br-0 plants expressing RBPG1 were equally susceptible as the recipient Br-0 to the necrotroph B. cinerea and to the biotroph Hyaloperonospora arabidopsidis. Pretreating leaves of the transgenic plants with a PG resulted in increased resistance to H. arabidopsidis. Coimmunoprecipitation experiments demonstrated that RBPG1 and PG form a complex in Nicotiana benthamiana, which also involves the Arabidopsis leucine-rich repeat receptor-like protein SOBIR1 (for SUPPRESSOR OF BIR1). sobir1 mutant plants did not induce necrosis in response to PGs and were compromised in PG-induced resistance to H. arabidopsidis.Microbe-associated molecular patterns (MAMPs) are molecular signatures of entire groups of microbes and have key roles in activation of the defense response in plants (Jones and Dangl, 2006; Boller and Felix, 2009). Well-characterized proteinaceous MAMPs are bacterial flagellin, Elongation Factor Tu (EF-Tu), and Ax21, fungal xylanase, and oomycete pep13, an epitope of a secreted transglutaminase (Boller and Felix, 2009; Monaghan and Zipfel, 2012). Plants recognize MAMPs by means of pattern recognition receptors (PRRs), comprising a group of leucine-rich repeat (LRR) receptor-like kinases (RLKs) or LRR receptor-like proteins (RLPs) located in the plasma membrane (Greeff et al., 2012; Monaghan and Zipfel, 2012). The LRR-RLKs FLS2 and EFR recognize flg22 (the 22-amino acid eliciting epitope from the conserved flagellin domain) and elf18/elf26 (peptides derived from the N terminus of translation elongation factor EF-Tu), respectively (Gómez-Gómez and Boller, 2000; Kunze et al., 2004; Chinchilla et al., 2006; Zipfel et al., 2006). The fungal protein ethylene-inducing xylanase (EIX) is recognized by the tomato (Solanum lycopersicum) LRR-RLPs LeEIX1 and LeEIX2, of which only the latter mediates a necrotic response (Ron and Avni, 2004).BRI1-ASSOCIATED KINASE1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE3 (BAK1/SERK3) is an LRR-RLK acting as a common component in many RLK signaling complexes (Monaghan and Zipfel, 2012). Although it was originally identified as a protein that interacts with the brassinosteroid receptor BRI1 (Li et al., 2002; Nam and Li, 2002), BAK1 also forms ligand-induced complexes with FLS2 and EFR and contributes to disease resistance against the pathogens Pseudomonas syringae, Hyaloperonospora arabidopsidis (Hpa), and Phytophthora infestans (Chinchilla et al., 2007; Heese et al., 2007; Chaparro-Garcia et al., 2011; Roux et al., 2011). Tomato BAK1 interacts in a ligand-independent manner with LeEIX1 but not with LeEIX2, and the BAK1-LeEIX1 interaction is required for the ability of LeEIX1 to attenuate the signaling of LeEIX2 (Bar et al., 2010). BAK1 has also been shown to interact with another LRR-RLK, BAK1-INTERACTING RECEPTOR-LIKE KINASE1 (BIR1). A bir1 mutant showed extensive cell death, activation of constitutive defense responses, and impairment in the activation of the mitogen-activated protein kinase MPK4 (Gao et al., 2009). sobir1 (for suppressor of BIR1) mutants suppress BIR1 phenotypes, and overexpression of SOBIR1 triggers cell death and defense responses (Gao et al., 2009). SOBIR1 does not physically interact with BIR1, suggesting that SOBIR1 mediates an alternative signal transduction route. A recent study showed that the tomato SOBIR1 interacts with RLPs and is required for RLP-mediated disease resistance (Liebrand et al., 2013).Endopolygalacturonases (PGs) are a class of pectinases that hydrolyze the homogalacturonan domain of pectic polysaccharides (van den Brink and de Vries, 2011). Secreted PGs are able to cause cell wall decomposition and tissue maceration and thereby act as virulence factors in several fungal pathogens, such as Aspergillus flavus, Claviceps purpurea, and Alternaria citri (Shieh et al., 1997; Isshiki et al., 2001; Oeser et al., 2002). The most extensively studied PGs from fungal plant pathogens are those of Botrytis cinerea (for review, see Zhang and van Kan, 2013b), a necrotrophic broad-host-range pathogen that contains six PG genes (designated Bcpg1–Bcpg6) in its genome (Wubben et al., 1999). Deletion of either Bcpg1 or Bcpg2 resulted in a strong reduction in virulence on tomato and broad bean (Vicia faba) leaves (ten Have et al., 1998; Kars et al., 2005), presumably because the enzymes have a detrimental effect on the integrity of host cell walls and tissues. Indeed, infiltrating BcPG2 into broad bean leaves or transient expression of BcPG2 in Nicotiana benthamiana led to tissue collapse and necrosis, and the necrotic response was abolished when the catalytic domain of the PG was mutated (Kars et al., 2005; Joubert et al., 2007). By contrast, Poinssot et al. (2003) reported that BcPG1 can activate plant defense responses in grapevine (Vitis vinifera) cell suspensions independently of its enzymatic activity, suggesting that the protein itself might be recognized by plant cells as an elicitor. These studies with seemingly opposing conclusions were conducted with different isozymes on distinct cell types of different plant species. Thus, it remained inconclusive whether plant responses observed after exposure to PGs are due to the structural damage resulting from pectin hydrolysis or to recognition of the protein as a MAMP (followed by downstream signaling responses).The degradation of pectin by PGs leads to the release of oligogalacturonides (OGAs), which may activate a variety of defense responses (Prade et al., 1999; D’Ovidio et al., 2004). OGAs act as damage-associated molecular patterns (DAMPs) via their perception by the cell wall-associated receptor Wall-Associated Kinase1 (WAK1; Brutus et al., 2010). Overexpression of WAK1 in Arabidopsis (Arabidopsis thaliana) enhances resistance to B. cinerea (Brutus et al., 2010).Here, we describe the occurrence of natural variation among Arabidopsis accessions in responsiveness to fungal PGs. Two accessions that strongly differed in their response to PGs were selected for further analysis. Cloning and functional characterization demonstrated that the gene RESPONSIVENESS TO BOTRYTIS POLYGALACTURONASES1 (RBPG1) encodes an LRR-RLP. Finally, we demonstrate that the LRR-RLK SUPPRESSOR OF BIR1 (SOBIR1) interacts with RBPG1 and is essential for responsiveness to fungal PGs.     

Ethylene is differentially regulated during sugar beet germination and affects early root growth in a dose-dependent manner

Main conclusion

By integrating molecular, biochemical, and physiological data, ethylene biosynthesis in sugar beet was shown to be differentially regulated, affecting root elongation in a concentration-dependent manner. There is a close relation between ethylene production and seedling growth of sugar beet (Beta vulgaris L.), yet the exact function of ethylene during this early developmental stage is still unclear. While ethylene is mostly considered to be a root growth inhibitor, we found that external 1-aminocyclopropane-1-carboxylic acid (ACC) regulates root growth in sugar beet in a concentration-dependent manner: low concentrations stimulate root growth while high concentrations inhibit root growth. These results reveal that ethylene action during root elongation is strongly concentration dependent. Furthermore our detailed study of ethylene biosynthesis kinetics revealed a very strict gene regulation pattern of ACC synthase (ACS) and ACC oxidase (ACO), in which ACS is the rate liming step during sugar beet seedling development.