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Morphological and genetic evidence for early Holocene cattle management in northeastern China
(2013)
The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent C-14 dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years.
Chirocephalus ruffoi is a fairy shrimp endemic to the Italian peninsula, where it is known only from thirteen high mountain locations. Twelve of these are in the Northern Apennines while the thirteenth is about 700 km away in the Calabrian Apennines (Southern Italy). We quantified degree of genetic divergence within the species by sequencing a fragment of the mitochondrial DNA encoding for Cytochrome Oxidase I. We then combined genetic data with the re-analysis of two different datasets on the morphometrics of the resting eggs (cysts) produced by the species as an adaptation to survive seasonal droughts. Genetic data revealed profound divergence; we identified four clusters of haplotypes within the species phylogeography, three in the Northern Apennines and one in the Calabrian Apennines with most of the genetic variation (a parts per thousand 70%) being apportioned among haplogroups. We found high variability in cyst morphometrics, especially in cyst size and height of the spines ornamenting the surface. Genetic and morphometric data are decoupled suggesting that cyst morphology is either under selection or a plastic trait. We, therefore, caution against using cyst morphology for taxonomic purposes in anostracans.
Time hierarchies, arising as a result of interactions between system's components, represent a ubiquitous property of dynamical biological systems. In addition, biological systems have been attributed switch-like properties modulating the response to various stimuli across different organisms and environmental conditions. Therefore, establishing the interplay between these features of system dynamics renders itself a challenging question of practical interest in biology. Existing methods are suitable for systems with one stable steady state employed as a well-defined reference. In such systems, the characterization of the time hierarchies has already been used for determining the components that contribute to the dynamics of biological systems. However, the application of these methods to bistable nonlinear systems is impeded due to their inherent dependence on the reference state, which in this case is no longer unique. Here, we extend the applicability of the reference-state analysis by proposing, analyzing, and applying a novel method, which allows investigation of the time hierarchies in systems exhibiting bistability. The proposed method is in turn used in identifying the components, other than reactions, which determine the systemic dynamical properties. We demonstrate that in biological systems of varying levels of complexity and spanning different biological levels, the method can be effectively employed for model simplification while ensuring preservation of qualitative dynamical properties (i.e., bistability). Finally, by establishing a connection between techniques from nonlinear dynamics and multivariate statistics, the proposed approach provides the basis for extending reference-based analysis to bistable systems.
Nitric oxide synthase (NOS) plays a critical role in a number of key physiological and pathological processes. Investigation of electron-transfer reactions in NOS would contribute to a better understanding of the nitric oxide (NO) synthesis mechanism. Herein, we describe an electrochemically driven catalytic strategy, using a nanocomposite that consisted of the oxygenase domain of neuronal NOS (D290nNOSoxy), indium tin oxide (ITO) nanopartides and polyvinyl alcohol (PVA). Fast direct electron transfer between electrodes and D290nNOSoxy was observed with the heterogeneous electron transfer rate constant (k(er)) of 154.8 +/- 0.1 s(-1) at the scan rate of 5 V s(-1). Moreover, the substrate IV-hydroxy-L-arginine (NHA) was used to prove the concept of electrochemically driven biocatalysis of D290nNOSoxy. In the presence of the oxygen cosubstrate and tetrahydrobiopterin (BH4) cofactor, the addition of NHA caused the decreases of both oxidation current at + 0.1 V and reduction current at potentials ranging from -0.149 V to -0.549 V vs Ag/AgCl. Thereafter, a series of control experiments such as in the absence of BH4 or D290nNOSoxy were performed. All the results demonstrated that D290nNOSoxy biocatalysis was successfully driven by electrodes in the presence of BH4 and oxygen. This novel bioelectronic system showed potential for further investigation of NOS and biosensor applications. (C) 2013 Elsevier B.V. All rights reserved.
Poststroke spasticity (PSS)-related disability is emerging as a significant health issue for stroke survivors. There is a need for predictors and early identification of PSS in order to minimize complications and maladaptation from spasticity. Reviewing the literature on stroke and upper motor neuron syndrome, spasticity, contracture, and increased muscle tone measured with the Modified Ashworth Scale and the Tone Assessment Scale provided data on the dynamic time course of PSS. Prevalence estimates of PSS were highly variable, ranging from 4% to 42.6%, with the prevalence of disabling spasticity ranging from 2% to 13%. Data on phases of the PSS continuum revealed evidence of PSS in 4% to 27% of those in the early time course (1-4 weeks poststroke), 19% to 26.7% of those in the postacute phase (1-3 months poststroke), and 17% to 42.6% of those in the chronic phase (>3 months poststroke). Data also identified key risk factors associated with the development of spasticity, including lower Barthel Index scores, severe degree of paresis, stroke-related pain, and sensory deficits. Although such indices could be regarded as predictors of PSS and thus enable early identification and treatment, the different measures of PSS used in those studies limit the strength of the findings. To optimize evaluation in the different phases of care, the best possible assessment of PSS would make use of a combination of indicators for clinical impairment, motor performance, activity level, quality of life, and patient-reported outcome measures. Applying these recommended measures, as well as increasing our knowledge of the physiologic predictors of PSS, will enable us to perform clinical and epidemiologic studies that will facilitate identification and early, multimodal treatment.
The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.
We investigated the morphology, phylogeny of the 18S rDNA, and pH response of Oxytricha acidotolerans sp. nov. and Urosomoida sp. (Ciliophora, Hypotricha) isolated from two chemically similar acid mining lakes (pH similar to 2.6) located at Langau, Austria, and in Lusatia, Germany. Oxytricha acidotolerans sp. nov. from Langau has 18 frontal-ventral-transverse cirri but a very indistinct kinety 3 fragmentation so that the assignment to Oxytricha is uncertain. The somewhat smaller species from Lusatia has a highly variable cirral pattern and the dorsal kineties arranged in the Urosomoida pattern and is, therefore, preliminary designated as Urosomoida sp. The pH response was measured as ciliate growth rates in laboratory experiments at pH ranging from 2.5 to 7.0. Our hypothesis was that the shape of the pH reaction norm would not differ between these closely related (3% difference in their SSU rDNA) species. Results revealed a broad pH niche for O. acidotolerans, with growth rates peaking at moderately acidic conditions (pH 5.2). Cyst formation was positively and linearly related to pH. Urosomoida sp. was more sensitive to pH and did not survive at circumneutral pH. Accordingly, we reject our hypothesis that similar habitats would harbour ciliate species with virtually identical pH reaction norm.
Multiple environmental stressors confine the ecological niche of the rotifer Cephalodella acidophila
(2013)
1The planktonic food web in extremely acidic mining lakes is restricted to a few species that are either acidophilic or acidotolerant. Common metazoans inhabiting acidic mining lakes with a pH below 3 include rotifers in the genera Cephalodella and Elosa. 2The life history response of Cephalodella acidophila to three environmental key factors, pH (2, 3.5, 5.0 and 7.0), temperature (10, 17.5 and 25 degrees C) and food concentration (10000, 35000 and 50000algal cells per mL), was investigated in a full factorial design using life-table experiments. 3The effect of each of the three environmental variables investigated on the rotifer life cycle parameters (life span, fecundity and population growth rate) differed. C.acidophila is a stenoecious species with a pH optimum in the range 34 and a comparably high food threshold. Combining the laboratory results with field data, we conclude that C.acidophila is severely growth limited in its natural habitat. However, low pH alone is not harmful as long as temperatures are moderate to warm and food is abundant. 4The population of C.acidophila in the field is maintained mainly due to release from competitors and predators.
Developmental senescence is a coordinated physiological process in plants and is critical for nutrient redistribution from senescing leaves to newly formed sink organs, including young leaves and developing seeds. Progress has been made concerning the genes involved and the regulatory networks controlling senescence. The resulting complex metabolome changes during senescence have not been investigated in detail yet. Therefore, we conducted a comprehensive profiling of metabolites, including pigments, lipids, sugars, amino acids, organic acids, nutrient ions, and secondary metabolites, and determined approximately 260 metabolites at distinct stages in leaves and siliques during senescence in Arabidopsis (Arabidopsis thaliana). This provided an extensive catalog of metabolites and their spatiotemporal cobehavior with progressing senescence. Comparison with silique data provides clues to source-sink relations. Furthermore, we analyzed the metabolite distribution within single leaves along the basipetal sink-source transition trajectory during senescence. Ceramides, lysolipids, aromatic amino acids, branched chain amino acids, and stress-induced amino acids accumulated, and an imbalance of asparagine/aspartate, glutamate/glutamine, and nutrient ions in the tip region of leaves was detected. Furthermore, the spatiotemporal distribution of tricarboxylic acid cycle intermediates was already changed in the presenescent leaves, and glucosinolates, raffinose, and galactinol accumulated in the base region of leaves with preceding senescence. These results are discussed in the context of current models of the metabolic shifts occurring during developmental and environmentally induced senescence. As senescence processes are correlated to crop yield, the metabolome data and the approach provided here can serve as a blueprint for the analysis of traits and conditions linking crop yield and senescence.
Aim In response to environmental changes and to avoid extinction, species may either track suitable environmental conditions or adapt to the modified environment. However, whether and how species adapt to environmental changes remains unclear. By focusing on the realized niche (i.e. the actual space that a species inhabits and the resources it can access as a result of limiting biotic factors present in its habitat), we here examine shifts in the realized-niche width (i.e. ecological amplitude) and position (i.e. ecological optimum) of 26 common and widespread forest understorey plants across their distributional ranges.
Location Temperate forests along a ca. 1800-km-long latitudinal gradient from northern France to central Sweden and Estonia.
Methods We derived species' realized-niche width from a -diversity metric, which increases if the focal species co-occurs with more species. Based on the concept that species' scores in a detrended correspondence analysis (DCA) represent the locations of their realized-niche positions, we developed a novel approach to run species-specific DCAs allowing the focal species to shift its realized-niche position along the studied latitudinal gradient while the realized-niche positions of other species were held constant.
Results None of the 26 species maintained both their realized-niche width and position along the latitudinal gradient. Few species (9 of 26: 35%) shifted their realized-niche width, but all shifted their realized-niche position. With increasing latitude, most species (22 of 26: 85%) shifted their realized-niche position for soil nutrients and pH towards nutrient-poorer and more acidic soils.
Main conclusions Forest understorey plants shifted their realized niche along the latitudinal gradient, suggesting local adaptation and/or plasticity. This macroecological pattern casts doubt on the idea that the realized niche is stable in space and time, which is a key assumption of species distribution models used to predict the future of biodiversity, hence raising concern about predicted extinction rates.
BACKGROUND: Mirror therapy (MT) was found to improve motor function after stroke, but its neural mechanisms remain unclear, especially in single stroke patients.
OBJECTIVES: The following imaging study was designed to compare brain activation patterns evoked by the mirror illusion in single stroke patients with normal subjects.
METHODS: Fifteen normal volunteers and five stroke patients with severe arm paresis were recruited. Cerebral activations during movement mirroring by means of a video chain were recorded with functional magnetic resonance imaging (fMRI). Single-subject analysis was performed using SPM 8.
RESULTS: For normal subjects, ten and thirteen subjects displayed lateralized cerebral activations evoked by the mirror illusion while moving their right and left hand respectively. The magnitude of this effect in the precuneus contralateral to the seen hand was not dependent on movement speed or subjective experience. Negative correlation of activation strength with age was found for the right hand only. The activation pattern in stroke patients is comparable to that of normal subjects and present in four out of five patients.
CONCLUSIONS: In summary, the mirror illusion can elicit cerebral activation contralateral to the perceived hand in the majority of single normal subjects, but not in all of them. This is similar even in stroke patients with severe hemiparesis.
Nodularia spumigena is a filamentous diazotrophic cyanobacterium that dominates the annual late summer cyanobacterial blooms in the Baltic Sea. But N. spumigena also is common in brackish water bodies worldwide, suggesting special adaptation allowing it to thrive at moderate salinities. A draft genome analysis of N. spumigena sp. CCY9414 yielded a single scaffold of 5,462,271 nucleotides in length on which genes for 5,294 proteins were annotated. A subsequent strand-specific transcriptome analysis identified more than 6,000 putative transcriptional start sites (TSS). Orphan TSSs located in intergenic regions led us to predict 764 non-coding RNAs, among them 70 copies of a possible retrotransposon and several potential RNA regulators, some of which are also present in other N2-fixing cyanobacteria. Approximately 4% of the total coding capacity is devoted to the production of secondary metabolites, among them the potent hepatotoxin nodularin, the linear spumigin and the cyclic nodulapeptin. The transcriptional complexity associated with genes involved in nitrogen fixation and heterocyst differentiation is considerably smaller compared to other Nostocales. In contrast, sophisticated systems exist for the uptake and assimilation of iron and phosphorus compounds, for the synthesis of compatible solutes, and for the formation of gas vesicles, required for the active control of buoyancy. Hence, the annotation and interpretation of this sequence provides a vast array of clues into the genomic underpinnings of the physiology of this cyanobacterium and indicates in particular a competitive edge of N. spumigena in nutrient-limited brackish water ecosystems.
Human-mediated dispersal is known as an important driver of long-distance dispersal for plants but underlying mechanisms have rarely been assessed. Road corridors function as routes of secondary dispersal for many plant species but the extent to which vehicles support this process remains unclear. In this paper we quantify dispersal distances and seed deposition of plant species moved over the ground by the slipstream of passing cars. We exposed marked seeds of four species on a section of road and drove a car along the road at a speed of 48 km/h. By tracking seeds we quantified movement parallel as well as lateral to the road, resulting dispersal kernels, and the effect of repeated vehicle passes. Median distances travelled by seeds along the road were about eight meters for species with wind dispersal morphologies and one meter for species without such adaptations. Airflow created by the car lifted seeds and resulted in longitudinal dispersal. Single seeds reached our maximum measuring distance of 45 m and for some species exceeded distances under primary dispersal. Mathematical models were fit to dispersal kernels. The incremental effect of passing vehicles on longitudinal dispersal decreased with increasing number of passes as seeds accumulated at road verges. We conclude that dispersal by vehicle airflow facilitates seed movement along roads and accumulation of seeds in roadside habitats. Dispersal by vehicle airflow can aid the spread of plant species and thus has wide implications for roadside ecology, invasion biology and nature conservation.
Newly determined Late Cretaceous Ar-40/Ar-39 ages on megacrystic kaersutite from four lamprophyre dikes, and a U-Pb zircon age on a trachyte, from central and north Westland (New Zealand) are presented. These ages suggest that the intrusion of mafic dikes (88-86 and 69 Ma) was not necessarily restricted to the previously established narrow age range of 80-92 Ma. The younger lamprophyre and trachyte dikes (c. 68-70 Ma) imply that tensional stresses in the Western Province were either renewed at this time, or that extension and related magmatism continued during opening of the Tasman Sea. Extension-related magmatism in the region not only preceded Tasman seafloor spreading initiation (starting at c. 83 Ma, lasting to c. 53 Ma), but may have sporadically continued for up to 15 Ma after continental break-up.
Understanding metabolic acclimation of plants to challenging environmental conditions is essential for dissecting the role of metabolic pathways in growth and survival. As stresses involve simultaneous physiological alterations across all levels of cellular organization, a comprehensive characterization of the role of metabolic pathways in acclimation necessitates integration of genome-scale models with high-throughput data. Here, we present an integrative optimization-based approach, which, by coupling a plant metabolic network model and transcriptomics data, can predict the metabolic pathways affected in a single, carefully controlled experiment. Moreover, we propose three optimization-based indices that characterize different aspects of metabolic pathway behavior in the context of the entire metabolic network. We demonstrate that the proposed approach and indices facilitate quantitative comparisons and characterization of the plant metabolic response under eight different light and/or temperature conditions. The predictions of the metabolic functions involved in metabolic acclimation of Arabidopsis thaliana to the changing conditions are in line with experimental evidence and result in a hypothesis about the role of homocysteine-to-Cys interconversion and Asn biosynthesis. The approach can also be used to reveal the role of particular metabolic pathways in other scenarios, while taking into consideration the entirety of characterized plant metabolism.
In recent years, an increasing number of mutations in what would appear to be 'housekeeping genes' have been identified as having unexpectedly specific defects in multicellular organogenesis. This is also the case for organogenesis in seed plants. Although it is not surprising that loss-of-function mutations in 'housekeeping' genes result in lethality or growth retardation, it is surprising when (1) the mutant phenotype results from the loss of function of a 'housekeeping' gene and (2) the mutant phenotype is specific. In this review, by defining housekeeping genes as those encoding proteins that work in basic metabolic and cellular functions, we discuss unexpected links between housekeeping genes and specific developmental processes. In a surprising number of cases housekeeping genes coding for enzymes or proteins with functions in basic cellular processes such as transcription, post-transcriptional modification, and translation affect plant development.
The M-type kinesin isoform, Kif9, has recently been implicated in maintaining a physical connection between the centrosome and nucleus in Dictyostelium discoideum. However, the mechanism by which Kif9 functions to link these two organelles remains obscure. Here we demonstrate that the Kif9 protein is localized to the nuclear envelope and is concentrated in the region underlying the centrosome point of attachment. Nuclear anchorage appears mediated through a specialized transmembrane domain located in the carboxyl terminus. Kif9 interacts with microtubules in in vitro binding assays and effects an endwise depolymerization of the polymer. These results suggest a model whereby Kif9 is anchored to the nucleus and generates a pulling force that reels the centrosome up against the nucleus. This is a novel activity for a kinesin motor, one important for progression of cells into mitosis and to ensure centrosome-nuclear parity in a multinuclear environment.
Floricolous downy mildews are a monophyletic group of members of the genus Peronospora (Oomycota, Peronosporales). These downy mildews can be found on a variety of families of the Asteridae, including Asteraceae, Campanulaceae, Dipsacaceae, Lamiaceae, and Orobanchaceae. With the exception of Peronospora radii, which can also cause economically relevant losses, sporulation usually takes place only on floral parts of their hosts. However, only very few specimens of these mostly inconspicuous downy mildews have so far been included in molecular phylogenies. Focusing on Lamiaceae, we have investigated multiple specimens of floricolous downy mildews for elucidating species boundaries and host specificity in this group. Based on both mitochondrial and nuclear loci, it became apparent that phylogenetic lineages in the Lamiaceae seem to be host genus specific and significant sequence diversity could be found between lineages. Based on distinctiveness in both phylogenetic reconstructions and morphology, the downy mildew on flowers of Stachys palustris is introduced as a new species, Peronospora jagei sp. nov., which can be morphologically distinguished from Peronospora stigmaticola by broader and shorter conidiospores. The diversity of the floricolous down mildews might be higher than previously assumed, although specimens from a much broader set of samples will be needed to confirm this view.
Background: Serotonin plays a pivotal role in regulating and modulating physiological and behavioral processes in both vertebrates and invertebrates. In the honeybee (Apis mellifera), serotonin has been implicated in division of labor, visual processing, and learning processes. Here, we present the cloning, heterologous expression, and detailed functional and pharmacological characterization of two honeybee 5-HT2 receptors.
Methods: Honeybee 5-HT2 receptor cDNAs were amplified from brain cDNA. Recombinant cell lines were established constitutively expressing receptor variants. Pharmacological properties of the receptors were investigated by Ca2+ imaging experiments. Quantitative PCR was applied to explore the expression patterns of receptor mRNAs.
Results: The honeybee 5-HT2 receptor class consists of two subtypes, Am5-HT2 alpha and Am5-HT2 beta. Each receptor gene also gives rise to alternatively spliced mRNAs that possibly code for truncated receptors. Only activation of the full-length receptors with serotonin caused an increase in the intracellular Ca2+ concentration. The effect was mimicked by the agonists 5-methoxytryptamine and 8-OH-DPAT at low micromolar concentrations. Receptor activities were blocked by established 5-HT receptor antagonists such as clozapine, methiothepin, or mianserin. High transcript numbers were detected in exocrine glands suggesting that 5-HT2 receptors participate in secretory processes in the honeybee.
Conclusions: This study marks the first molecular and pharmacological characterization of two 5-HT2 receptor subtypes in the same insect species. The results presented should facilitate further attempts to unravel central and peripheral effects of serotonin mediated by these receptors.
This study focuses on the evolutionary relationships among Turkish species of the cave cricket genus Troglophilus. Fifteen populations were studied for sequence variation in a fragment (543 base pairs) of the mitochondrial DNA (mtDNA) 16S rDNA gene (16S) to reconstruct their phylogenetic relationships and biogeographic history. Genetic data retrieved three main clades and at least three divergent lineages that could not be attributed to any of the taxa known for the area. Molecular time estimates suggest that the diversification of the group took place between the Messinian and the Plio-Pleistocene.
A unified understanding of the relationship between disturbance and biodiversity is needed to predict biotic responses to global change. Recent advances have identified the need to deconstruct traditional models of disturbance into intensity and frequency to reconcile empirical studies that appear to generate contradictory associations between species diversity and disturbance. We integrate results from theoretical simulation modelling, field-based surveys of 5176 vegetation plots from 48 transects across 6 sites, and experimental pot-based manipulations of flooding to identify how disturbance drives species diversity within ephemeral wetlands in South Island, New Zealand. We find empirical, hump-shaped and positive relationships between species diversity and both disturbance intensity and frequency, mirroring patterns from a simulation model in which species differed in their demographic responses to disturbance. More generally, our simulations show that the relationships between diversity and disturbance shift from positive to hump-shaped to negative as species that are favored at low disturbance because of their resistance strategies, defined by low mortality and recruitment, decline within communities relative to resilient species. Resilient species with higher mortality and recruitment rates are instead favored as disturbance intensity and frequency intensify. Our theoretical findings suggest that sites must also have a third group of unique species with intermediate resilience and resistance. Analyses of community composition along our disturbance gradients support this prediction, emphasizing that shifts in community-level resistance and resilience drive empirical associations between diversity and disturbance. Overall, terrestrial plants may be unable to resist intense and frequent flooding, even with specialized traits. Only fast-growing species with high regeneration from seed may respond once flooding subsides and dominate community composition in these situations, especially on nutrient-rich soils. However, different strategies can co-occur at intermediate disturbance, ultimately increasing species richness. As disturbances become more pervasive globally, our results suggest that differences in the niches of species, rather than demographic stochasticity, drive biodiversity patterns. These niche-based processes may especially prevail, without accompanying losses in species richness, where sites are initially dominated by resistant taxa or life history strategies that balance resistance and resilience.
Natural genetic diversity provides a powerful tool to study the complex interrelationship between metabolism and growth. Profiling of metabolic traits combined with network-based and statistical analyses allow the comparison of conditions and identification of sets of traits that predict biomass. However, it often remains unclear why a particular set of metabolites is linked with biomass and to what extent the predictive model is applicable beyond a particular growth condition. A panel of 97 genetically diverse Arabidopsis (Arabidopsis thaliana) accessions was grown in near-optimal carbon and nitrogen supply, restricted carbon supply, and restricted nitrogen supply and analyzed for biomass and 54 metabolic traits. Correlation-based metabolic networks were generated from the genotype-dependent variation in each condition to reveal sets of metabolites that show coordinated changes across accessions. The networks were largely specific for a single growth condition. Partial least squares regression from metabolic traits allowed prediction of biomass within and, slightly more weakly, across conditions (cross-validated Pearson correlations in the range of 0.27-0.58 and 0.21-0.51 and P values in the range of <0.001-<0.13 and <0.001-<0.023, respectively). Metabolic traits that correlate with growth or have a high weighting in the partial least squares regression were mainly condition specific and often related to the resource that restricts growth under that condition. Linear mixed-model analysis using the combined metabolic traits from all growth conditions as an input indicated that inclusion of random effects for the conditions improves predictions of biomass. Thus, robust prediction of biomass across a range of conditions requires condition-specific measurement of metabolic traits to take account of environment-dependent changes of the underlying networks.
The twin-arginine translocation (TAT) pathway of the bacterial cytoplasmic membrane mediates translocation only of proteins that accomplished a native-like conformation. We deploy this feature in modular selection systems for directed evolution, in which folding helpers as well as dimeric or oligomeric proteinprotein interactions enable TAT-dependent translocation of the resistance marker TEM -lactamase (L). Specifically, we demonstrate and analyze selection of (i) enhancers for folding by direct TAT translocation selection of a target protein interposed between the TorA signal sequence and L, (ii) dimeric or oligomeric proteinprotein interactions by hitchhiker translocation (HiT) selection of proteins fused to the TorA signal sequence and to the L, respectively and (iii) heterotrimeric proteinprotein interactions by combining HiT with protein fragment complementation selection of proteins fused to two split L fragments and TorA, respectively. The lactamase fragments were additionally engineered for improved activity and stability. Applicability was benchmarked with interaction partners of known affinity and multimerization whereby cellular fitness correlated well with biophysical protein properties. Ultimately, the HiT selection was employed to identify peptides, which specifically bind to leukemia- and melanoma-relevant target proteins (MITF and ETO) by coiled-coil or tetra-helix-bundle formation with high affinity. The various versions of TAT selection led to inhibiting peptides (iPEPs) of disease-promoting interactions and enabled so far difficult to achieve selections.
Mean age of carbon in fine roots from temperate forests and grasslands with different management
(2013)
Fine roots are the most dynamic portion of a plant's root system and a major source of soil organic matter. By altering plant species diversity and composition, soil conditions and nutrient availability, and consequently belowground allocation and dynamics of root carbon (C) inputs, land-use and management changes may influence organic C storage in terrestrial ecosystems. In three German regions, we measured fine root radiocarbon (C-14) content to estimate the mean time since C in root tissues was fixed from the atmosphere in 54 grassland and forest plots with different management and soil conditions. Although root biomass was on average greater in grasslands 5.1 +/- 0.8 g (mean +/- SE, n = 27) than in forests 3.1 +/- 0.5 g (n = 27) (p < 0.05), the mean age of C in fine roots in forests averaged 11.3 +/- 1.8 yr and was older and more variable compared to grasslands 1.7 +/- 0.4 yr (p < 0.001). We further found that management affects the mean age of fine root C in temperate grasslands mediated by changes in plant species diversity and composition. Fine root mean C age is positively correlated with plant diversity (r = 0.65) and with the number of perennial species (r = 0.77). Fine root mean C age in grasslands was also affected by study region with averages of 0.7 +/- 0.1 yr (n= 9) on mostly organic soils in northern Germany and of 1.8 +/- 0.3 yr (n = 9) and 2.6 +/- 0.3 (n = 9) in central and southern Germany (p < 0.05). This was probably due to differences in soil nutrient contents and soil moisture conditions between study regions, which affected plant species diversity and the presence of perennial species. Our results indicate more long-lived roots or internal redistribution of C in perennial species and suggest linkages between fine root C age and management in grasslands. These findings improve our ability to predict and model belowground C fluxes across broader spatial scales.
The relationship of different types of grassland use with plant species richness and composition ( functional groups of herbs, legumes, and grasses) has so far been studied at small regional scales or comprising only few components of land use. We comprehensively studied the relationship between abandonment, fertilization, mowing intensity, and grazing by different livestock types on plant diversity and composition of 1514 grassland sites in three regions in North-East, Central and South-West Germany. We further considered environmental site conditions including soil type and topographical situation. Fertilized grasslands showed clearly reduced plant species diversity (-15% plant species richness, -0.1 Shannon diversity on fertilized grasslands plots of 16m(2)) and changed composition (-3% proportion of herb species), grazing had the second largest effects and mowing the smallest ones. Among the grazed sites, the ones grazed by sheep had higher than average species richness (+27%), and the cattle grazed ones lower (-42%). Further, these general results were strongly modulated by interactions between the different components of land use and by regional context: land-use effects differed largely in size and sometimes even in direction between regions. This highlights the importance of comparing different regions and to involve a large number of plots
Recent phylogenetic analyses show that the species of the southern African genera Pauridia, Saniella and Spiloxene and the Australian, Tasmanian and New Zealand Hypoxis sect. Ianthe form a highly supported, monophyletic clade. In keeping with earlier suggestions that these taxa doubtfully warrant separate status, and to avoid the recognition of Hypoxis and Spiloxene as paraphyletic, we expand the circumscription of Pauridia to include Saniella, Spiloxene and Hypoxis sect. Ianthe. As a result 33 new combinations at specific and infraspecific level are proposed and one epitype, two neotypes and 30 lectotypes are newly designated. Three basionyms, of which Linnaeus, Linnaeus filius and Lamarck are the authors, are also typified (Amaryllis capensis, Hypoxis aquatica, and Hypoxis pumila).
Ag-TiO2 and Au-TiO2 hybrid electrodes were designed by covalent attachment of TiO2 nanoparticles to Ag or Au electrodes via an organic linker. The optical and electronic properties of these systems were investigated using the cytochrome b(5) (Cyt b(5)) domain of sulfite oxidase, exclusively attached to the TiO2 surface, as a Raman marker and model redox enzyme. Very strong SERR signals of Cyt b(5) were obtained for Ag-supported systems due to plasmonic field enhancement of Ag. Time-resolved surface-enhanced resonance Raman spectroscopic measurements yielded a remarkably fast electron transfer kinetic (k = 60 s(-1)) of Cyt b(5) to Ag. A much lower Raman intensity was observed for Au-supported systems with undefined and slow redox behavior. We explain this phenomenon on the basis of the different potential of zero charge of the two metals that largely influence the electronic properties of the TiO2 island film.
Disturbances' role in shaping communities is well documented but highly disputed. We suggest replacing the overused two-trait trade-off approach with a functional group scheme, constructed from combinations of four key traits that represent four classes of species' responses to disturbances. Using model results and field observations from sites affected by two highly different disturbances, we demonstrated that popular dichotomous trade-offs are not sufficient to explain community dynamics, even if some emerge under certain conditions. Without disturbances, competition was only sufficient to predict species survival but not relative success, which required some escape mechanism (e.g., long-term dormancy). With highly predictable and large-scale disturbances, successful species showed a combination of high individual tolerance to disturbance and, more surprisingly, high competitive ability. When disturbances were less predictable, high individual tolerance and long-term seed dormancy were favored, due to higher environmental uncertainty. Our study demonstrates that theories relying on a small number of predefined trade-offs among traits (e.g., competition-colonization trade-off) may lead to unrealistic results. We suggest that the understanding of disturbance-community relationships can be significantly improved by employing sets of relevant trait assemblies instead of the currently common approach in which trade-offs are assumed in advance.
The persistence of species under changed climatic conditions depends on adaptations and plastic responses to these conditions and on interactions with their local plant community resulting in direct and indirect effects of changed climatic conditions. Populations at species' range margins may be especially crucial in containing a gene pool comprising adaptations to extreme climatic conditions. Many species of northern European bog ecosystems reach their southern lowland range limit in central Europe. In a common-garden experiment, we experimentally assessed the impact of projected climatic changes on five bog-plant species (including peat moss Sphagnum magellanicum) sampled along a latitudinal gradient of 1400km from Scandinavia to the marginal lowland populations in Germany. Populations were cultivated in monocultures and in experimental communities composed of all five species from their local community, and exposed to five combinations of three climate treatments (warming, fluctuating water-tables, fertilization) in a southern common garden. Whereas most monocultures showed a decreasing biomass production from southern to northern origins under southern environmental conditions, in the experimental mixed-species communities, an increasing biomass production towards northern communities was observed together with a shift in interspecific interactions along the latitudinal gradient. While negative dominance effects prevailed in southern communities, higher net biodiversity effects were observed in northern subarctic communities. The combined effects of climate treatments increased biomass production in monocultures of most origins. In communities, however, overall the treatments did not result in significantly changed biomass production. Among individual treatments, water-table fluctuations caused a significant decrease in biomass production, but only in southern communities, indicating higher vulnerability to changed climatic conditions. Here, negative effects of climate treatments on graminoids were not compensated by the slightly increased growth of peat moss that benefited from interspecific interactions only in northern communities.Synthesis. We conclude that shifting interactions within multispecies communities caused pronounced responses to changed climatic conditions in wetland communities of temperate southern marginal, but not of northern subarctic origin. Therefore, future models investigating the impacts of climate change on plant communities should consider geographical variation in species interactions an important factor influencing community responses to changed climatic conditions.
The digital laser rangefinder GLM Professional (R) BOSCH 250 VF was tested as a modified preproduction model with regard to its applicability of quantifying humans' height. The aim of this investigation was to determine and evaluate the instrument's precision, as well as its manageability within anthropometric field studies. Data collected by the digital laser rangefinder did not show a significant difference to data of control by an anthropometer. Furthermore, more than 96% of the difference values are located within area of agreement. Nevertheless, the GLM Professional (R) is a highly sensitive instrument and mean SD within threefold data acquisition is twice as high as SD resulting from data collection by an anthropometer. However, due to the minimal percentage differences within data acquisition and compared to the standard method, the GLM Professional (R) is proved to be a reliable instrument and to be highly applicable for anthropometric field studies. Furthermore, due to its excellent manageability and compact size, the GLM Professional (R) shows a very good applicability even for less trained anthropometrists and thus ameliorates the possibilities of collecting reliable data within anthropometric field studies.
The hydrolytic degradation and corresponding content release of capsules made of poly(d,l-lactic-co-glycolic acid) (PLGA) strongly depends on the composition and material properties of the initially applied copolymer. Consecutive or simultaneous release from capsule batches of combinable material compositions, therefore, offers high control over the bioavailability of an encapsulated drug. The keynote of this study was the creation of a superordinated database that addressed the correlation between the release kinetics of filling agents with different molecular weights from PLGA capsules of alternating composition. Fluorescein isothiocyanate (FITC)-dextran (with molecular weights of 4, 40, and 2000 kDa) was chosen as a model analyte, whereas the copolymers were taken from various 50:50 PLGA, 75:25 PLGA, and polylactide blends. With reference to recent publications, the capsule properties, such as the size, morphology, and encapsulation efficiency, were further modified during production. Hence, uniform microdisperse and polydisperse submicrometer nanocapsules were prepared by two different water-in-oil-in-water emulsification techniques, and additional effects on the size and morphology were achieved by capsule solidification in two different sodium salt buffers. The qualitative and quantitative examination of the physical capsule properties was performed by confocal laser scanning microscopy, scanning electron microscopy, and Coulter counting techniques to evaluate the capsule size distribution and the morphological appearance of the different batches. The corresponding agent release was quantified by fluorescence measurement of the FITC-dextran in the incubation media and by the direct measurement of the capsule brightness via fluorescence microscopy. In summary, the observed agent release showed a highly controllable flexibility depending on the PLGA blends, preparation methods, and molecular weight of the used filling substances. (c) 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 130: 4219-4228, 2013
Phosphorylation and dephosphorylation of starch and glycogen are important for their physicochemical properties and also their physiological functions. It is therefore desirable to reliably determine the phosphorylation sites. Heteronuclear multidimensional NMR-spectroscopy is in principle a straightforward analytical approach even for complex carbohydrate molecules. With heterogeneous samples from natural sources, however, the task becomes more difficult because a full assignment of the resonances of the carbohydrates is impossible to obtain. Here, we show that the combination of heteronuclear H-1,C-13 and H-1,C-13,P-31 techniques and information derived from spectra of a set of reference compounds can lead to an unambiguous determination of the phosphorylation sites even in heterogeneous samples.
Growth regulation is an important aspect of plant adaptation during environmental perturbations. Here, the role of MULTIPASS (OsMPS), an R2R3-type MYB transcription factor of rice, was explored. OsMPS is induced by salt stress and expressed in vegetative and reproductive tissues. Over-expression of OsMPS reduces growth under non-stress conditions, while knockdown plants display increased biomass. OsMPS expression is induced by abscisic acid and cytokinin, but is repressed by auxin, gibberellin and brassinolide. Growth retardation caused by OsMPS over-expression is partially restored by auxin application. Expression profiling revealed that OsMPS negatively regulates the expression of EXPANSIN (EXP) and cell-wall biosynthesis as well as phytohormone signaling genes. Furthermore, the expression of OsMPS-dependent genes is regulated by auxin, cytokinin and abscisic acid. Moreover, we show that OsMPS is a direct upstream regulator of OsEXPA4, OsEXPA8, OsEXPB2, OsEXPB3, OsEXPB6 and the endoglucanase genes OsGLU5 and OsGLU14. The multiple responses of OsMPS and its target genes to various hormones suggest an integrative function of OsMPS in the cross-talk between phytohormones and the environment to regulate adaptive growth.
Early detection of salt stress is vital for plant survival and growth. Still, the molecular processes controlling early salt stress perception and signaling are not fully understood. Here, we identified SALT-RESPONSIVE ERF1 (SERF1), a rice (Oryza sativa) transcription factor (TF) gene that shows a root-specific induction upon salt and hydrogen peroxide (H2O2) treatment. Loss of SERF1 impairs the salt-inducible expression of genes encoding members of a mitogen-activated protein kinase (MAPK) cascade and salt tolerance-mediating TFs. Furthermore, we show that SERF1-dependent genes are H2O2 responsive and demonstrate that SERF1 binds to the promoters of MAPK KINASE KINASE6 (MAP3K6), MAPK5, DEHYDRATION-RESPONSIVE ELEMENT BINDING2A (DREB2A), and ZINC FINGER PROTEIN179 (ZFP179) in vitro and in vivo. SERF1 also directly induces its own gene expression. In addition, SERF1 is a phosphorylation target of MAPK5, resulting in enhanced transcriptional activity of SERF1 toward its direct target genes. In agreement, plants deficient for SERF1 are more sensitive to salt stress compared with the wild type, while constitutive overexpression of SERF1 improves salinity tolerance. We propose that SERF1 amplifies the reactive oxygen species-activated MAPK cascade signal during the initial phase of salt stress and translates the salt-induced signal into an appropriate expressional response resulting in salt tolerance.
279 bat specimens of 14 species were examined for ectoparasites during the autumnal swarming period in different cave roosts in Albania. A total of 550 ectoparasites were identified belonging to 19 species. The structure of the ectoparasite fauna and the influence of body mass index and body surface area on the parasite load were discussed for the most common bat species (Miniopterus schreibersii, Myotis myotis, M. capaccinii and Rhinolophus ferrumequinum). The ectoparasite fauna of the studied bats in Albania is qualitatively similar to northern Bulgaria (SCHEFFLER, 2011). The bat species Myotis myotis and M. daubentonii are infested with different ectoparasites in the Balkan region during the autumn swarming period than specimens of the same bat species in Central Europe. There is a strong need of further research for most host and ectoparasite species in the entire Balkan region.
Types of Body Shape
(2013)
The human face shows individual features and features that are characteristic for sex and age (the loss of childlike characteristics during maturation). The analysis of facial dimensions is essential for identifying individual features also for forensic issues.
The analysis of facial proportions was performed on photogrammetric data from front views of 125 children. The data were pooled from 2 different studies. The children's data were obtained from a longitudinal study and reduced by random generator to ensure the data of adults from a separate cross-sectional study.
We applied principal component analysis on photogrammetric facial proportions of 169 individuals: 125 children (63 boys and 62 girls) aged 2-7 years and 44 adults (18 men and 26 women) aged 18-65 years.
Facial proportions depend on age and sex. Three components described age: (1) proportions of facial height to head height, (2) proportions that involve endocanthal breadth, and (3) bigonial to bizygonial proportions. Proportions that associate with sex are connected with nasal distances and nasal to bizygonial distances.
Twenty-three percent of the variance, particularly variance that are connected with proportions of lower and middle face heights to head height, do neither depend on sex nor on age and thus appear useful for screening purposes, eg, for dysmorphic genetic syndromes.
Body composition
(2013)
Biological age
(2013)
Eastern Mediterranean ecosystems are prone to desertification when under grazing pressure. Therefore, management of grazing intensity plays a crucial role to avoid or to diminish land degradation and to sustain both livelihoods and ecosystem functioning. The dynamic land-use model LandSHIFT was applied to a case study on the country level for Jordan. The impacts of different stocking densities on the environment were assessed through a set of simulation experiments for various combinations of climate input and assumptions about the development of livestock numbers. Indicators used for the analysis include a set of landscape metrics to account for habitat fragmentation and the "Human Appropriation of Net Primary Production" (HANPP), i.e., the difference between the amount of net primary production (NPP) that would be available in a natural ecosystem and the amount of NPP that remains under human management. Additionally, the potential of the economic valuation of ecosystem services, including landscape and grazing services, as an analysis concept was explored. We found that lower management intensities had a positive effect on HANPP but at the same time resulted in a strong increase of grazing area. This effect was even more pronounced under climate change due to a predominantly negative effect on the biomass productivity of grazing land. Also Landscape metrics tend to indicate decreasing habitat fragmentation as a consequence of lower grazing pressure. The valuation of ecosystem services revealed that low grazing intensity can lead to a comparatively higher economic value on the country level average. The results from our study underline the importance of considering grazing management as an important factor to manage dry-land ecosystems in a sustainable manner.
Open porous foams with identical foam density but different pore-size distributions (bimodal or monomodal) are prepared from a shape-memory polyetherurethane (PEU) by thermally induced phase separation. The shape-memory effect of the two PEU foams is explored by cyclic thermomechanical compression tests and microstructural analysis. The obtained results reveal that the PEU foam with a bimodal pore-size distribution exhibits an increased shape-recovery under stress-free conditions, both on the macro- (foam level) as well as the microscale (pore level). While bimodal pore-size distributions induce microscale bending during compression, buckling occurs in foams with monomodal pore-size distributions, leading to both a reduced and delayed shape recovery.
Aim To assess how habitat loss and climate change interact in affecting the range dynamics of species and to quantify how predicted range dynamics depend on demographic properties of species and the severity of environmental change. Location South African Cape Floristic Region. Methods We use data-driven demographic models to assess the impacts of past habitat loss and future climate change on range size, range filing and abundances of eight species of woody plants (Proteaceae). The species-specific models employ a hybrid approach that simulates population dynamics and long-distance dispersal on top of expected spatio-temporal dynamics of suitable habitat. Results Climate change was mainly predicted to reduce range size and range filling (because of a combination of strong habitat shifts with low migration ability). In contrast, habitat loss mostly decreased mean local abundance. For most species and response measures, the combination of habitat loss and climate change had the most severe effect. Yet, this combined effect was mostly smaller than expected from adding or multiplying effects of the individual environmental drivers. This seems to be because climate change shifts suitable habitats to regions less affected by habitat loss. Interspecific variation in range size responses depended mostly on the severity of environmental change, whereas responses in range filling and local abundance depended mostly on demographic properties of species. While most surviving populations concentrated in areas that remain climatically suitable, refugia for multiple species were overestimated by simply overlying habitat models and ignoring demography. Main conclusions Demographic models of range dynamics can simultaneously predict the response of range size, abundance and range filling to multiple drivers of environmental change. Demographic knowledge is particularly needed to predict abundance responses and to identify areas that can serve as biodiversity refugia under climate change. These findings highlight the need for data-driven, demographic assessments in conservation biogeography.
Calcium (Ca2+) is a ubiquitous intracellular second messenger and involved in a plethora of cellular processes. Thus, quantification of the intracellular Ca2+ concentration ([Ca2+](i)) and of its dynamics is required for a comprehensive understanding of physiological processes and potential dysfunctions. A powerful approach for studying [Ca2+](i) is the use of fluorescent Ca2+ indicators. In addition to the fluorescence intensity as a common recording parameter, the fluorescence lifetime imaging microscopy (FLIM) technique provides access to the fluorescence decay time of the indicator dye. The nanosecond lifetime is mostly independent of variations in dye concentration, allowing more reliable quantification of ion concentrations in biological preparations. In this study, the feasibility of the fluorescent Ca2+ indicator Oregon Green Bapta-1 (OGB-1) for two-photon fluorescence lifetime imaging microscopy (2P-FLIM) was evaluated. In aqueous solution, OGB-1 displayed a Ca2+-dependent biexponential fluorescence decay behaviour, indicating the presence of a Ca2+-free and Ca2+-bound dye form. After sufficient dye loading into living cells, an in situ calibration procedure has also unravelled the Ca2+-free and Ca2+-bound dye forms from a global biexponential fluorescence decay analysis, although the dye's Ca2+ sensitivity is reduced. Nevertheless, quantitative [Ca2+](i) recordings and its stimulus-induced changes in salivary gland cells could be performed successfully. These results suggest that OGB-1 is suitable for 2P-FLIM measurements, which can gain access to cellular physiology.
Cell-free protein synthesis (CFPS) is a valuable method for the fast expression of difficult-to-express proteins as well as posttranslationally modified proteins. Since cell-free systems circumvent possible cytotoxic effects caused by protein overexpression in living cells, they significantly enlarge the scale and variety of proteins that can be characterized. We demonstrate the high potential of eukaryotic CFPS to express various types of membrane proteins covering a broad range of structurally and functionally diverse proteins. Our eukaryotic cell-free translation systems are capable to provide high molecular weight membrane proteins, fluorescent-labeled membrane proteins, as well as posttranslationally modified proteins for further downstream analysis.
Polymers exhibiting cell-selective effects represent an extensive research field with high relevance for biomedical applications e.g. in the cardiovascular field supporting re-endothelialization while suppressing smooth muscle cell overgrowth. Such an endothelial cell-selective effect could be recently demonstrated for a copolyetheresterurethane (PDC) containing biodegradable poly(p-dioxanone) and poly(epsilon-caprolactone) segments, which selectively enhanced the adhesion of human umbilical vein endothelial cells (HUVEC) while suppressing the attachment of smooth muscle cells (SMC).
In this study we investigated the influence of the fibre orientation (random and aligned) and fibre diameter (2 mu m and 500 nm) of electrospun PDC scaffolds on the adhesion, proliferation and apoptosis of HUVEC and SMC.
Adhesion, viability and proliferation of HUVEC was diminished when the fibre diameter was reduced to a submicron scale, while the orientation of the microfibres did only slightly influence the cellular behaviour. In contrast, a submicron fibre diameter improved SMC viability. In conclusion, PDC scaffolds with micron-sized single fibres could be promising candidate materials for cell-selective stent coatings.
Controlled conversion of leaf starch to sucrose at night is essential for the normal growth of Arabidopsis. The conversion involves the cytosolic metabolism of maltose to hexose phosphates via an unusual, multidomain protein with 4-glucanotransferase activity, DPE2, believed to transfer glucosyl moieties to a complex heteroglycan prior to their conversion to hexose phosphate via a cytosolic phosphorylase. The significance of this complex pathway is unclear; conversion of maltose to hexose phosphate in bacteria proceeds via a more typical 4-glucanotransferase that does not require a heteroglycan acceptor. It has recently been suggested that DPE2 generates a heterogeneous series of terminal glucan chains on the heteroglycan that acts as a glucosyl buffer to ensure a constant rate of sucrose synthesis in the leaf at night. Alternatively, DPE2 and/or the heteroglycan may have specific properties important for their function in the plant. To distinguish between these ideas, we compared the properties of DPE2 with those of the Escherichia coli glucanotransferase MalQ. We found that MalQ cannot use the plant heteroglycan as an acceptor for glucosyl transfer. However, experimental and modeling approaches suggested that it can potentially generate a glucosyl buffer between maltose and hexose phosphate because, unlike DPE2, it can generate polydisperse malto-oligosaccharides from maltose. Consistent with this suggestion, MalQ is capable of restoring an essentially wild-type phenotype when expressed in mutant Arabidopsis plants lacking DPE2. In light of these findings, we discuss the possible evolutionary origins of the complex DPE2-heteroglycan pathway.
MADS-domain transcription factors have been shown to act as key repressors or activators of the transition to flowering and as master regulators of reproductive organ identities. Despite their important roles in plant development, the origin of several MADS-box subfamilies has remained enigmatic so far. Here we demonstrate, through a combination of genome synteny and phylogenetic reconstructions, the origin of three major, apparently angiosperm-specific MADS-box gene clades: FLOWERING LOCUS C- (FLC-), SQUAMOSA- (SQUA-) and SEPALLATA- (SEP-) -like genes. We find that these lineages derive from a single ancestral tandem duplication in a common ancestor of extant seed plants. Contrary to common belief, we show that FLC- like genes are present in cereals where they can also act as floral repressors responsive to prolonged cold or vernalization. This opens a new perspective on the translation of findings from Arabidopsis to cereal crops, in which vernalization was originally described.
Objectives: Obesity and a reduced physical activity are global developments. Physical activity affects the external skeletal robustness which decreased in German children. It was assumed that the negative trend of decreased external skeletal robustness can be found in other countries. Therefore anthropometric data of Russian and German children from the years 2000 and 2010 were compared.
Methods: Russian (2000/2010 n = 1023/268) and German (2000/2010 n = 2103/1750) children aged 6-10 years were investigated. Height, BMI and external skeletal robustness (Frame-Index) were examined and compared for the years and the countries. Statistical analysis was performed by Mann-Whitney-Test.
Results: Comparison 2010 and 2000: In Russian children BMI was significantly higher; boys were significantly taller and exhibited a decreased Frame-Index (p = .002) in 2010. German boys showed significantly higher BMI in 2010. In both sexes Frame-Index (p = .001) was reduced in 2010. Comparison Russian and German children in 2000: BMI, height and Frame-Index were different between Russian and German children. German children were significantly taller but exhibited a lower Frame-Index (p<.001). Even German girls showed a significantly higher BMI. Comparison Russian and German children in 2010: BMI and Frame-Index were different. Russian children displayed a higher Frame-Index (p<.001) compared with Germans.
Conclusions: In Russian children BMI has increased in recent years. Frame-Index is still higher in Russian children compared with Germans however in Russian boys Frame-Index is reduced. This trend and the physical activity should be observed in the future.
Objectives Childhood obesity is a global problem, e.g., due to physical inactivity. External skeletal robustness (Frame-Index) has decreased in German schoolchildren. An association between Frame-Index and physical activity was assumed. Further often body mass index (BMI) is analyzed without reference to bone structure. Therefore, we analyze relationships between Frame-Index, BMI, % body fat, and physical activity. Methods In a cross-sectional study, 691 German children aged 610 years were investigated. BMI, % body fat, Frame-Index, total steps p.w., sports club rate p.w., training time p.d., and TV-time p.d. were determined. Results Total steps (P<0.001), BMI (P<0.001), and % body fat (P=0.024) are positively linked to Frame-Index. Total steps (P<0.001), sports club rate (P=0.001), and training time (P<0.001) are negatively associated with % body fat. Total steps (P=0.017) are negatively linked to BMI. TV-time is positively related to BMI (P<0.001) and % body fat (P<0.001). % Body fat is affected by age (P<0.001), sex (P=0.028), and total steps (P=0.002). BMI is influenced by age (P<0.001), and Frame-Index by sex (P<0.001) and total steps (P=0.029). Principal component analysis indicates an association between BMI and TV-time and Frame-Index and total steps. Conclusions We demonstrate an association between external skeletal robustness and physical activity, which is not captured by in BMI measurements. Children should be physically active in order to maintain skeletal robustness. Am. J. Hum. Biol. 25:404410, 2013.
The molybdenum cofactor is an important cofactor, and its biosynthesis is essential for many organisms, including humans. Its basic form comprises a single molybdopterin (MPT) unit, which binds a molybdenum ion bearing three oxygen ligands via a dithiolene function, thus forming Mo-MPT. In bacteria, this form is modified to form the bis-MPT guanine dinucleotide cofactor with two MPT units coordinated at one molybdenum atom, which additionally contains GMPs bound to the terminal phosphate group of the MPTs (bis-MGD). The MobA protein catalyzes the nucleotide addition to MPT, but the mechanism of the biosynthesis of the bis-MGD cofactor has remained enigmatic. We have established an in vitro system for studying bis-MGD assembly using purified compounds. Quantification of the MPT/molybdenum and molybdenum/phosphorus ratios, time-dependent assays for MPT and MGD detection, and determination of the numbers and lengths of Mo-S and Mo-O bonds by X-ray absorption spectroscopy enabled identification of a novel bis-Mo-MPT intermediate on MobA prior to nucleotide attachment. The addition of Mg-GTP to MobA loaded with bis-Mo-MPT resulted in formation and release of the final bis-MGD product. This cofactor was fully functional and reconstituted the catalytic activity of apo-TMAO reductase (TorA). We propose a reaction sequence for bis-MGD formation, which involves 1) the formation of bis-Mo-MPT, 2) the addition of two GMP units to form bis-MGD on MobA, and 3) the release and transfer of the mature cofactor to the target protein TorA, in a reaction that is supported by the specific chaperone TorD, resulting in an active molybdoenzyme.
Sulfite oxidase (SO) is an essential molybdoenzyme for humans, catalyzing the final step in the degradation of sulfur-containing amino acids and lipids, which is the oxidation of sulfite to sulfate. The catalytic site of SO consists of a molybdenum ion bound to the dithiolene sulfurs of one molybdopterin (MPT) molecule, carrying two oxygen ligands, and is further coordinated by the thiol sulfur of a conserved cysteine residue. We have exchanged four non-active site cysteines in the molybdenum cofactor (Moco) binding domain of human SO (SOMD) with serine using site-directed mutagenesis. This facilitated the specific replacement of the active site Cys207 with selenocysteine during protein expression in Escherichia coli. The sulfite oxidizing activity (k(cat)/K-M) of SeSOMD4Ser was increased at least 1.5-fold, and the pH optimum was shifted to a more acidic value compared to those of SOMD4Ser and SOMD4Cys(wt) X-ray absorption spectroscopy revealed a Mow Se bond length of 2.51 A, likely caused by the specific binding of Sec207 to the molybdenum, and otherwise rather similar square-pyramidal S/Se(Cys)(O2MoS2)-S-VI(MPT) site structures in the three constructs. The low-pH form of the Mo(V) electron paramagnetic resonance (EPR) signal of SeSOM4Ser was altered compared to those of SOMD4Ser and SOMD4cy,(,), with g, in particular shifted to a lower magnetic field, due to the Se ligation at the molybdenum. In contrast, the Mo(V) EPR signal of the high-pH form was unchanged. The substantially stronger effect of substituting selenocysteine for cysteine at low pH as compared to high pH is most likely due to the decreased covalency of the Mo Se bond.
Honey bees are important model organisms for neurobiology, because they display a large array of behaviors. To link behavior with individual gene function, quantitative polymerase chain reaction is frequently used. Comparing gene expression of different individuals requires data normalization using adequate reference genes. These should ideally be expressed stably throughout lifetime. Unfortunately, this is frequently not the case. We studied how well three commonly used reference genes are suited for this purpose and measured gene expression in the brains of honey bees differing in age and social role. Although rpl32 is used most frequently, it only remains stable in expression between newly emerged bees, nurse-aged bees, and pollen foragers but shows a peak at the age of 12 days. The genes gapdh and ef1 alpha-f1, in contrast, are expressed stably in the brain throughout all age groups except newly emerged bees. According to stability software, gapdh was expressed most stably, followed by rpl32 and ef1 alpha-f1.
Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
In rosette plants, root flooding (waterlogging) triggers rapid upward (hyponastic) leaf movement representing an important architectural stress response that critically determines plant performance in natural habitats. The directional growth is based on localized longitudinal cell expansion at the lower (abaxial) side of the leaf petiole and involves the volatile phytohormone ethylene (ET). We report the existence of a transcriptional core unit underlying directional petiole growth in Arabidopsis thaliana, governed by the NAC transcription factor SPEEDY HYPONASTIC GROWTH (SHYG). Overexpression of SHYG in transgenic Arabidopsis thaliana enhances waterlogging-triggered hyponastic leaf movement and cell expansion in abaxial cells of the basal petiole region, while both responses are largely diminished in shyg knockout mutants. Expression of several EXPANSIN and XYLOGLUCAN ENDOTRANSGLYCOSYLASE/HYDROLASE genes encoding cell wall-loosening proteins was enhanced in SHYG overexpressors but lowered in shyg. We identified ACC OXIDASE5 (ACO5), encoding a key enzyme of ET biosynthesis, as a direct transcriptional output gene of SHYG and found a significantly reduced leaf movement in response to root flooding in aco5 T-DNA insertion mutants. Expression of SHYG in shoot tissue is triggered by root flooding and treatment with ET, constituting an intrinsic ET-SHYG-ACO5 activator loop for rapid petiole cell expansion upon waterlogging.
ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription
(2013)
Leaf senescence is a key physiological process in all plants. Its onset is tightly controlled by transcription factors, of which NAC factor ORE1 (ANAC092) is crucial in Arabidopsis thaliana. Enhanced expression of ORE1 triggers early senescence by controlling a downstream gene network that includes various senescence-associated genes. Here, we report that unexpectedly ORE1 interacts with the G2-like transcription factors GLK1 and GLK2, which are important for chloroplast development and maintenance, and thereby for leaf maintenance. ORE1 antagonizes GLK transcriptional activity, shifting the balance from chloroplast maintenance towards deterioration. Our finding identifies a new mechanism important for the control of senescence by ORE1.
Studies explaining the choice of model structure for population viability analysis (PVA) are rare and no such study exists for butterfly species, a focal group for conservation. Here, we describe in detail the development of a model to predict population viability of a glacial relict butterfly species, Boloria eunomia, under climate change. We compared four alternative formulations of an individual-based model, differing in the environmental factors acting on the survival of immature life stages: temperature (only temperature impact), weather (temperature, precipitation, and sunshine), temperature and parasitism, and weather and parasitism. Following pattern-oriented modeling, four observed patterns were used to contrast these models: one qualitative (response of population size to habitat parameters) and three quantitative ones describing population dynamics during eight years (mean and variability of population size, and magnitude of the temporal autocorrelation in yearly population growth rates). The four model formulations were not equally able to depict population dynamics under current environmental conditions; the model including only temperature was selected as the most parsimonious model sufficiently well reproducing the empirical patterns. We used all four model formulations to test a range of climate change scenarios that were characterized by changes in both mean and variability of the weather variables. All models predicted adverse effects of climate change and resulted in the same ranking of mean climate change scenarios. However, models differed in their absolute values of population viability measures, underlining the need to explicitly choose the most appropriate model formulation and avoid arbitrary usage of environmental drivers in a model. We conclude that further applications of pattern-oriented modeling to butterfly and other species are likely to help in identifying the key factors impacting the viability of certain taxa, which, ultimately, will aid and speed up informed management decisions for endangered species under climate change.
Aim Seed banks are central to the regeneration strategy of many plant species. Any factor altering seed bank density thus affects plant regeneration and population dynamics. Although seed banks are dynamic entities controlled by multiple environmental drivers, climatic factors are the most comprehensive, but still poorly understood. This study investigates how climatic variation structures seed production and resulting seed bank patterns.
Location Temperate forests along a 1900km latitudinal gradient in north-western (NW) Europe.
Methods Seed production and seed bank density were quantified in 153 plots along the gradient for four forest herbs with different seed longevity: Geum urbanum, Milium effusum, Poa nemoralis and Stachys sylvatica. We tested the importance of climatic and local environmental factors in shaping seed production and seed bank density.
Results Seed production was determined by population size, and not by climatic factors. G.urbanum and M.effusum seed bank density declined with decreasing temperature (growing degree days) and/or increasing temperature range (maximum-minimum temperature). P.nemoralis and S.sylvatica seed bank density were limited by population size and not by climatic variables. Seed bank density was also influenced by other, local environmental factors such as soil pH or light availability. Different seed bank patterns emerged due to differential seed longevities. Species with long-lived seeds maintained constant seed bank densities by counteracting the reduced chance of regular years with high seed production at colder northern latitudes.
Main conclusions Seed bank patterns show clear interspecific variation in response to climate across the distribution range. Not all seed banking species may be as well equipped to buffer climate change via their seed bank, notably in short-term persistent species. Since the buffering capacity of seed banks is key to species persistence, these results provide crucial information to advance climatic change predictions on range shifts, community and biodiversity responses.
We investigated mechanisms of reproductive isolation in livebearing fishes (genus Poecilia) inhabiting sulfidic and nonsulfidic habitats in three replicate river drainages. Although sulfide spring fish convergently evolved divergent phenotypes, it was unclear if mechanisms of reproductive isolation also evolved convergently. Using microsatellites, we found strongly reduced gene flow between adjacent populations from different habitat types, suggesting that local adaptation to sulfidic habitats repeatedly caused the emergence of reproductive isolation. Reciprocal translocation experiments indicate strong selection against immigrants into sulfidic waters, but also variation among drainages in the strength of selection against immigrants into nonsulfidic waters. Mate choice experiments revealed the evolution of assortative mating preferences in females from nonsulfidic but not from sulfidic habitats. The inferred strength of sexual selection against immigrants (RIs) was negatively correlated with the strength of natural selection (RIm), a pattern that could be attributed to reinforcement, whereby natural selection strengthens behavioral isolation due to reduced hybrid fitness. Overall, reproductive isolation and genetic differentiation appear to be replicated and direct consequences of local adaptation to sulfide spring environments, but the relative contributions of different mechanisms of reproductive isolation vary across these evolutionarily independent replicates, highlighting both convergent and nonconvergent evolutionary trajectories of populations in each drainage.
Semi-natural grasslands, biodiversity hotspots in Central-Europe, suffer from the cessation of traditional land-use. Amount and intensity of these changes challenge current monitoring frameworks typically based on classic indicators such as selected target species or diversity indices. Indicators based on plant functional traits provide an interesting extension since they reflect ecological strategies at individual and ecological processes at community levels. They typically show convergent responses to gradients of land-use intensity over scales and regions, are more directly related to environmental drivers than diversity components themselves and enable detecting directional changes in whole community dynamics. However, probably due to their labor- and cost intensive assessment in the field, they have been rarely applied as indicators so far.
Here we suggest overcoming these limitations by calculating indicators with plant traits derived from online accessible databases. Aiming to provide a minimal trait set to monitor effects of land-use intensification on plant diversity we investigated relationships between 12 community mean traits, 2 diversity indices and 6 predictors of land-use intensity within grassland communities of 3 different regions in Germany (part of the German 'Biodiversity Exploratory' research network). By standardization of traits and diversity measures, use of null models and linear mixed models we confirmed (i) strong links between functional community composition and plant diversity, (ii) that traits are closely related to land-use intensity, and (iii) that functional indicators are equally, or even more sensitive to land-use intensity than traditional diversity indices. The deduced trait set consisted of 5 traits, i.e., specific leaf area (SLA), leaf dry matter content (LDMC), seed release height, leaf distribution, and onset of flowering. These database derived traits enable the early detection of changes in community structure indicative for future diversity loss. As an addition to current monitoring measures they allow to better link environmental drivers to processes controlling community dynamics.
The ability of some chemical compounds to cause oxidative stress offers a fast and convenient way to study the responses of plants to reactive oxygen species (ROS). In order to unveil potential novel genetic players of the ROS-regulatory network, a population of similar to 2,000 randomly selected Arabidopsis thaliana T-DNA insertion mutants was screened for ROS sensitivity/resistance by growing seedlings on agar medium supplemented with stress-inducing concentrations of the superoxide-eliciting herbicide methyl viologen or the catalase inhibitor 3-amino-triazole. A semi-robotic setup was used to capture and analyze images of the chemically treated seedlings which helped interpret the screening results by providing quantitative information on seedling area and healthy-to-chlorotic tissue ratios for data verification. A ROS-related phenotype was confirmed in three of the initially selected 33 mutant candidates, which carry T-DNA insertions in genes encoding a Ring/Ubox superfamily protein, ABI5 binding protein 1 (AFP1), previously reported to be involved in ABA signaling, and a protein of unknown function, respectively. In addition, we identified six mutants, most of which have not been described yet, that are related to growth or chloroplast development and show defects in a ROS-independent manner. Thus, semi-automated image capturing and phenotyping applied on publically available T-DNA insertion collections adds a simple means for discovering novel mutants in complex physiological processes and identifying the genes involved.
A population of Luisia curtisii (Orchidaceae: Aeridinae) in northern Thailand was studied with regard to pollination biology. Although a high level of self-compatibility was demonstrated experimentally, the very low natural fruit set (1.4-1.9 %) clearly indicated that the species depends on external agents for pollination. Our observations suggest that L. curtisii is pollinated by beetles, as Lema unicolor (Chrysomelidae) and Clinteria ducalis (Scarabaeidae) were the only flower visitors observed to carry pollinaria of this species. The hypothesis of specialised cantharophily is further supported by 2-methylbutyric acid and caproic acid being striking components of the floral scent. Judging from the lack of nectar and the behaviour of visiting beetles, the pollination system seems to rely on food or brood site deception. Retention of the anther on the pollinarium for some time after pollinarium removal probably reduces the frequency of insect-mediated autogamy and geitonogamy in Luisia curtisii-a possibility that was supported by comparative data on (1) the anther retention time and inflorescence visitation time of Lema unicolor and (2) stigma and anther length in the orchid. Existing reports of specialised beetle pollination in orchids are reviewed, and we conclude that there is accumulating evidence that specialised cantharophily is more common in the Orchidaceae than previously assumed.
Introduction: We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces.
Results: Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set.
Conclusions: We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.
Talitrids are the only family within the order Amphipoda to have colonised supralittoral and terrestrial environments. They live in a variety of settings, from sandy to rocky and pebble beaches, to river and lake banks, and to leaf litter and caves. A common feature is the absence of a planktonic larval stage to facilitate passive dispersal over long-distances. However, some species have broad distributions. Genetic studies over the past 25 years have tried to explain this apparent contradiction by assessing patterns of species genetic structuring on different geographical scales. Here, we review the molecular studies available to date and focus on the population genetics of talitrids. Most of these studies considered populations in the Mediterranean area, but also along the Atlantic coast and in Canary Island caves. From this review, the group emerges as a potential model to understand processes of dispersal and divergence in non-highly-vagile supralittoral organisms. At the same time, studies on these issues are still too restricted geographically: a worldwide scale including different regions would provide us with a better perspective on these problems.
Molecular phenotyping technologies (e.g., transcriptomics, proteomics, and metabolomics) offer the possibility to simultaneously obtain multivariate time series (MTS) data from different levels of information processing and metabolic conversions in biological systems. As a result, MTS data capture the dynamics of biochemical processes and components whose couplings may involve different scales and exhibit temporal changes. Therefore, it is important to develop methods for determining the time segments in MTS data, which may correspond to critical biochemical events reflected in the coupling of the system's components. Here we provide a novel network-based formalization of the MTS segmentation problem based on temporal dependencies and the covariance structure of the data. We demonstrate that the problem of partitioning MTS data into k segments to maximize a distance function, operating on polynomially computable network properties, often used in analysis of biological network, can be efficiently solved. To enable biological interpretation, we also propose a breakpoint-penalty (BP-penalty) formulation for determining MTS segmentation which combines a distance function with the number/length of segments. Our empirical analyses of synthetic benchmark data as well as time-resolved transcriptomics data from the metabolic and cell cycles of Saccharomyces cerevisiae demonstrate that the proposed method accurately infers the phases in the temporal compartmentalization of biological processes. In addition, through comparison on the same data sets, we show that the results from the proposed formalization of the MTS segmentation problem match biological knowledge and provide more rigorous statistical support in comparison to the contending state-of-the-art methods.
Effects of intraspecific and community density on the lifetime fecundity of long-lived shrubs
(2013)
Intra- and interspecific density dependence has profound consequences for plant population and community dynamics. In long-lived plants, however, lifetime patterns and mechanisms of density dependence are difficult to study. Here, we examine effects of intraspecific and community density on the lifetime fecundity of two long-lived shrub species from South African Fynbos: Protea repens (animal-pollinated, hermaphroditic) and Leucadendron rubrum (wind-pollinated, dioecious). Both species are serotinous, retaining seeds in cones until fire kills the mother plant. We measured lifetime fecundity as the product of cone number, proportion of cones that are not damaged by predation and seed set (fertile seeds per intact cone). Intraspecific and community densities were quantified by counting individuals of target species and all Proteaceae in small- and large-scale neighbourhoods (10 m and 50 m radius) around each focal individual. Additionally, we determined the age and size of focal individuals. We found that lifetime fecundity of the wind-pollinated L rubrum is density independent. In contrast, the lifetime fecundity of the animal-pollinated P. repens increases with large-scale intraspecific density and shows a hump-shaped relationship to large-scale community density. Community density has a hump-shaped effect on seed set (probably through partial absence of generalized pollinators at low and competition for pollinators at high densities) and negatively affects cone number per individual. For both species, plant age decreases seed set while increasing lifetime fecundity. The qualitative differences in the density dependence of lifetime fecundity may arise from differences between animal and wind pollination. In particular, interactions with generalized animal pollinators may cause community-level Allee effects with profound consequences for the future dynamics of long-lived plant populations and communities.
Laforin or malin deficiency causes Lafora disease, characterized by altered glycogen metabolism and teenage-onset neurodegeneration with intractable and invariably fatal epilepsy. Plant starches possess small amounts of metabolically essential monophosphate esters. Glycogen contains similar phosphate amounts, which are thought to originate from a glycogen synthase error side reaction and therefore lack any specific function. Glycogen is also believed to lack monophosphates at glucosyl carbon C6, an essential phosphorylation site in plant starch metabolism. We now show that glycogen phosphorylation is not due to a glycogen synthase side reaction, that C6 is a major glycogen phosphorylation site, and that C6 monophosphates predominate near centers of glycogen molecules and positively correlate with glycogen chain lengths. Laforin or malin deficiency causes C6 hyperphosphorylation, which results in malformed long-chained glycogen that accumulates in many tissues, causing neurodegeneration in brain. Our work advances the understanding of Lafora disease pathogenesis and suggests that glycogen phosphorylation has important metabolic function.
In both animal and plant kingdoms, body size is a fundamental but still poorly understood attribute of biological systems. Here we report that the Arabidopsis NAC transcription factor Regulator of Proteasomal Gene Expression' (RPX) controls leaf size by positively modulating proteasome activity. We further show that the cis-element recognized by RPX is evolutionarily conserved between higher plant species. Upon over-expression of RPX, plants exhibit reduced growth, which may be reversed by a low concentration of the pharmacological proteasome inhibitor MG132. These data suggest that the rate of protein turnover during growth is a critical parameter for determining final organ size.
Isolation of recombinant antibodies from antibody libraries is commonly performed by different molecular display formats including phage display and ribosome display or different cell-surface display formats. We describe a new method which allows the selection of Escherichia coil cells producing the required single chain antibody by cultivation in presence of ampicillin conjugated to the antigen of interest. The method utilizes the neutralization of the conjugate by the produced single chain antibody which is secreted to the periplasm. Therefore, a new expression system based on the pET26b vector was designed and a library was constructed. The method was successfully established first for the selection of E. coli BL21 Star (DE3) cells expressing a model single chain antibody (anti-fluorescein) by a simple selection assay on LB-agar plates. Using this selection assay, we could identify a new single chain antibody binding biotin by growing E. coil BL21 Star (DE3) containing the library in presence of a biotin-ampicillin conjugate. In contrast to methods as molecular or cell surface display our selection system applies the soluble single chain antibody molecule and thereby avoids undesired effects, e.g. by the phage particle or the yeast fusion protein. By selecting directly in an expression strain, production and characterization of the selected single chain antibody is possible without any further cloning or transformation steps.
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the stoichiometry of the underlying interrelated components, but also on the multitude of kinetic parameters. Invariant flux ratios, obtained within flux coupling analysis, as well as invariant complex ratios, derived within chemical reaction network theory, can characterize robust properties of a system at steady state. However, the existing formalisms for the description of these invariants do not provide full characterization as they either only focus on the flux-centric or the concentration-centric view. Here we develop a novel mathematical framework which combines both views and thereby overcomes the limitations of the classical methodologies. Our unified framework will be helpful in analyzing biologically important system properties.
The geological history of the Ponto-Caspian region, with alternating cycles of isolation and reconnection among the three main basins (Black and Azov Seas, and the more distant Caspian Sea) as well as between them and the Mediterranean Sea, profoundly affected the diversification of its aquatic fauna, leading to a high degree of endemism. Two alternative hypotheses on the origin of this amazing biodiversity have been proposed, corresponding to phases of allopatric separation of aquatic fauna among sea basins: a Late Miocene origin (10-6 MYA) vs. a more recent Pleistocene ancestry (<2 MYA). Both hypotheses support a vicariant origin of (1) Black + Azov Sea lineages on the one hand, and (2) Caspian Sea lineages on the other. Here, we present a study on the Ponto-Caspian endemic amphipod Pontogammarus maeoticus. We assessed patterns of divergence based on (a) two mitochondrial and one nuclear gene, and (b) a morphometric analysis of 23 morphological traits in 16 populations from South and West Caspian Sea, South Azov Sea and North-West Black Sea. Genetic data indicate a long and independent evolutionary history, dating back from the late Miocene to early Pleistocene (6.6-1.6 MYA), for an unexpected, major split between (i) a Black Sea clade and (ii) a well-supported clade grouping individuals from the Caspian and Azov Seas. Absence of shared haplotypes argues against either recent or human-mediated exchanges between Caspian and Azov Seas. A mismatch distribution analysis supports more stable population demography in the Caspian than in the Black Sea populations. Morphological divergence largely followed patterns of genetic divergence: our analyses grouped samples according to the basin of origin and corroborated the close phylogenetic affinity between Caspian and Azov Sea lineages. Altogether, our results highlight the necessity of careful (group-specific) evaluation of evolutionary trajectories in marine taxa that should certainly not be inferred from the current geographical proximity of sea basins alone. (C) 2013 Elsevier Inc. All rights reserved.
Although the DNA methyltransferase 2 family is highly conserved during evolution and recent reports suggested a dual specificity with stronger activity on transfer RNA (tRNA) than DNA substrates, the biological function is still obscure. We show that the Dictyostelium discoideum Dnmt2-homologue DnmA is an active tRNA methyltransferase that modifies C38 in tRNA(Asp(GUC)) in vitro and in vivo. By an ultraviolet-crosslinking and immunoprecipitation approach, we identified further DnmA targets. This revealed specific tRNA fragments bound by the enzyme and identified tRNA(Glu(CUC/UUC)) and tRNA(Gly(GCC)) as new but weaker substrates for both human Dnmt2 and DnmA in vitro but apparently not in vivo. Dnmt2 enzymes form transient covalent complexes with their substrates. The dynamics of complex formation and complex resolution reflect methylation efficiency in vitro. Quantitative PCR analyses revealed alterations in dnmA expression during development, cell cycle and in response to temperature stress. However, dnmA expression only partially correlated with tRNA methylation in vivo. Strikingly, dnmA expression in the laboratory strain AX2 was significantly lower than in the NC4 parent strain. As expression levels and binding of DnmA to a target in vivo are apparently not necessarily accompanied by methylation, we propose an additional biological function of DnmA apart from methylation.
Integrated and concurrent cultures in rice fields are a promising approach to sustainable farming as the demand for aquacultural and agricultural products continues to grow while land and water resources become increasingly scarce. Prawn farming mainly takes place in coastal regions in improved extensive to semi-intensive aquacultures but a trend to shift the industry to inland regions has been noticed. This inland study in Northern Bangladesh used different input regimes such as fertilizer and additional feed to compare the performance of prawn and fish in flooded paddy fields in regard to water quality measurements. Maximal net yields and body weight gain with minimized negative impact on water quality were found when initial body weights of prawn were optimized. Regarding yield factors in reference to the reduction of costs due to the avoidance of expensive fertilizer/feed and effort, prawn performed better than integrated fish cultures considering a higher market value of prawn with net yields of up to 97 +/- 55 kg ha(-1) for unfed and 151 +/- 61 kg ha(-1) for fed treatments. Rice yields of up to 4.7 +/- 0.1 t ha(-1) for unfed and 4.4 +/- 0.1 t ha(-1) were achieved for fed treatments. The findings suggest that for small scale farmers, prawn cum rice cultures are an economically profitable and comparatively easily manageable alternative to rice cum fish cultures.
A species of Galapagos tortoise endemic to Espanola Island was reduced to just 12 females and three males that have been bred in captivity since 1971 and have produced over 1700 offspring now repatriated to the island. Our molecular genetic analyses of juveniles repatriated to and surviving on the island indicate that none of the tortoises sampled in 1994 had hatched on the island versus 3% in 2004 and 24% in 2007, which demonstrates substantial and increasing reproduction in situ once again. This recovery occurred despite the parental population having an estimated effective population size <8 due to a combination of unequal reproductive success of the breeders and nonrandom mating in captivity. These results provide guidelines for adapting breeding regimes in the parental captive population and decreasing inbreeding in the repatriated population. Using simple morphological data scored on the sampled animals, we also show that a strongly heterogeneous distribution of tortoise sizes on Espanola Island observed today is due to a large variance in the number of animals included in yearly repatriation events performed in the last 40years. Our study reveals that, at least in the short run, some endangered species can recover dramatically despite a lack of genetic variation and irregular repatriation efforts.
The generation of antibodies with designated specificity requires cost-intensive and time-consuming screening procedures. Here we present a new method by which hybridoma cells can be selected based on the specificity of the produced antibody by the use of antigen-toxin-conjugates thus eliminating the need of a screening procedure. Initial experiments were done with methotrexate as low molecular weight toxin and fluorescein as model antigen. Methotrexate and a methotrexate-fluorescein conjugate were characterized regarding their toxicity. Afterwards the effect of the fluorescein-specific antibody B13-DE1 on the toxicity of the methotrexate-fluorescein conjugate was determined. Finally, first results showed that hybridoma cells that produce fluorescein specific antibodies are able to grow in the presence of fluorescein-toxin-conjugates.
Contamination of soil with toxic heavy metals poses a major threat to the environment and human health. Anthropogenic sources include smelting of ores, municipal wastes, fertilizers, and pesticides. In assessing soil quality and the environmental and ecological risk of contamination with heavy metals, often homogeneous contamination of the soil is assumed. However, soils are very heterogeneous environments. Consequently, both contamination and the response of soil organisms can be assumed to be heterogeneous. This might have consequences for the exposure of soil organisms and for the extrapolation of risk from the individual to the population level. Therefore, to explore how soil contamination of different spatial heterogeneity affects population dynamics of soil invertebrates, we developed a spatially explicit individual-based model of the springtail, Folsomia candida, a standard test species for ecotoxicological risk assessment. In the model, individuals were assumed to sense and avoid contaminated habitat with a certain probability that depends on contamination level. Avoidance of contaminated areas thus influenced the individuals' movement and feeding, their exposure, and in turn all other biological processes underlying population dynamics. Model rules and parameters were based on data from the literature, or were determined via pattern-oriented modelling. The model correctly predicted several patterns that were not used for model design and calibration. Simulation results showed that the ability of the individuals to detect and avoid the toxicant, combined with the presence of clean habitat patches which act as "refuges", made equilibrium population size due to toxic effects less sensitive to increases in toxicant concentration. Additionally, the level of heterogeneity among patches of soil (i.e. the difference in concentration) was important: at the same average concentration, a homogeneously contaminated scenario was the least favourable habitat, while higher levels of heterogeneity corresponded to higher population growth rate and equilibrium size. Our model can thus be used as a tool for extrapolating from short-term effects at the individual level to long-term effects at the population level under more realistic conditions. It can thus be used to develop and extrapolate from standard ecotoxicological tests in the laboratory to ecological risk assessments.
The impact of environmental stimuli on the production of the widespread cyanobacterial hepatotoxin microcystin (MC) is under debate. Whereas transcriptional studies of the biosynthetic genes suggest a clear influence of light conditions on toxin production the data for the metabolite itself are inconsistent and highly strain-specific. Here, we have reassessed the MC content by using two immunological detection techniques that allow a parallel quantification of MC in the methanolic extracts and the residual pellet fraction that contains high molecular weight proteins. Our results show a significant proportion of MC in the protein bound fraction in strains of Microcystis and Planktothrix and of the related toxin nodularin (NOD) in Nodularia. Moreover, we could show a very strong increase of MC after high light illumination in the protein fraction contributing to a significant overall increase in MC production under these conditions that is not seen in extracts analysed by LC-MS and ELISA. The fact that a considerable portion of MC is neglected with current analysis techniques was also confirmed for selected field samples. Immunofluorescence studies suggest strain-specific differences in the amount of MC conjugate formation.
We report about ERF BUD ENHANCER (EBE; At5g61890), a transcription factor that affects cell proliferation as well as axillary bud outgrowth and shoot branching in Arabidopsis (Arabidopsis thaliana). EBE encodes a member of the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor superfamily; the gene is strongly expressed in proliferating cells and is rapidly and transiently up-regulated in axillary meristems upon main stem decapitation. Overexpression of EBE promotes cell proliferation in growing calli, while the opposite is observed in EBE-RNAi lines. EBE overexpression also stimulates axillary bud formation and outgrowth, while repressing it results in inhibition of bud growth. Global transcriptome analysis of estradiol-inducible EBE overexpression lines revealed 48 EBE early-responsive genes, of which 14 were up-regulated and 34 were downregulated. EBE activates several genes involved in cell cycle regulation and dormancy breaking, including D-type cyclin CYCD3; 3, transcription regulator DPa, and BRCA1-ASSOCIATED RING DOMAIN1. Among the down-regulated genes were DORMANCY-ASSOCIATED PROTEIN1 (AtDRM1), AtDRM1 homolog, MEDIATOR OF ABA-REGULATED DORMANCY1, and ZINC FINGER HOMEODOMAIN5. Our data indicate that the effect of EBE on shoot branching likely results from an activation of genes involved in cell cycle regulation and dormancy breaking.
Understanding the regional dynamics of plant communities is crucial for predicting the response of plant diversity to habitat fragmentation. However, for fragmented landscapes the importance of regional processes, such as seed dispersal among isolated habitat patches, has been controversially debated. Due to the stochasticity and rarity of among-patch dispersal and colonization events, we still lack a quantitative understanding of the consequences of these processes at the landscape-scale. In this study, we used extensive field data from a fragmented, semi-arid landscape in Israel to parameterize a multi-species incidence-function model. This model simulates species occupancy pattern based on patch areas and habitat configuration and explicitly considers the locations and the shapes of habitat patches for the derivation of patch connectivity. We implemented an approximate Bayesian computation approach for parameter inference and uncertainty assessment. We tested which of the three types of regional dynamics - the metacommunity, the mainland-island, or the island communities type - best represents the community dynamics in the study area and applied the simulation model to estimate the extinction debt in the investigated landscape. We found that the regional dynamics in the patch-matrix study landscape is best represented as a system of highly isolated island' communities with low rates of propagule exchange among habitat patches and consequently low colonization rates in local communities. Accordingly, the extinction rates in the local communities are the main drivers of community dynamics. Our findings indicate that the landscape carries a significant extinction debt and in model projections 33-60% of all species went extinct within 1000 yr. Our study demonstrates that the combination of dynamic simulation models with field data provides a promising approach for understanding regional community dynamics and for projecting community responses to habitat fragmentation. The approach bears the potential for efficient tests of conservation activities aimed at mitigating future losses of biodiversity.
Quantifying the association of plant functional traits to environmental gradients is a promising approach for understanding and projecting community responses to land use and climatic changes. Although habitat fragmentation and climate are expected to affect plant communities interactively, there is a lack of empirical studies addressing trait associations to fragmentation in different climatic regimes.
In this study, we analyse data on the key functional traits: specific leaf area (SLA), plant height, seed mass and seed number. First, we assess the evidence for the community assembly mechanisms habitat filtering and competition at different spatial scales, using several null-models and a comprehensive set of community-level trait convergence and divergence indices. Second, we analyse the association of community-mean traits with patch area and connectivity along a south-north productivity gradient.
We found clear evidence for trait convergence due to habitat filtering. In contrast, the evidence for trait divergence due to competition fundamentally depended on the null-model used. When the null-model controlled for habitat filtering, there was only evidence for trait divergence at the smallest sampling scale (0.25 m x 0.25 m). All traits varied significantly along the S-N productivity gradient. While plant height and SLA were consistently associated with fragmentation, the association of seed mass and seed number with fragmentation changed along the S-N gradient.
Our findings indicate trait convergence due to drought stress in the arid sites and due to higher productivity in the mesic sites. The association of plant traits to fragmentation is likely driven by increased colonization ability in small and/or isolated patches (plant height, seed number) or increased persistence ability in isolated patches (seed mass).
Our study provides the first empirical test of trait associations with fragmentation along a productivity gradient. We conclude that it is crucial to study the interactive effects of different ecological drivers on plant functional traits.
The NAC transcription factor ORE1 is a key regulator of senescence in Arabidopsis thaliana. Here, we demonstrate that senescence-induced and cell death-associated BIFUNCTIONAL NUCLEASE1 (BFN1) is a direct downstream target of ORE1, revealing a previously unknown regulatory cascade.Senescence is a highly regulated process that involves the action of a large number of transcription factors. The NAC transcription factor ORE1 (ANAC092) has recently been shown to play a critical role in positively controlling senescence in Arabidopsis thaliana; however, no direct target gene through which it exerts its molecular function has been identified previously. Here, we report that BIFUNCTIONAL NUCLEASE1 (BFN1), a well-known senescence-enhanced gene, is directly regulated by ORE1. We detected elevated expression of BFN1 already 2 h after induction of ORE1 in estradiol-inducible ORE1 overexpression lines and 6 h after transfection of Arabidopsis mesophyll cell protoplasts with a 35S:ORE1 construct. ORE1 and BFN1 expression patterns largely overlap, as shown by promoterreporter gene (GUS) fusions, while BFN1 expression in senescent leaves and the abscission zones of maturing flower organs was virtually absent in ore1 mutant background. In vitro binding site assays revealed a bipartite ORE1 binding site, similar to that of ORS1, a paralog of ORE1. A bipartite ORE1 binding site was identified in the BFN1 promoter; mutating the cis-element within the context of the full-length BFN1 promoter drastically reduced ORE1-mediated transactivation capacity in transiently transfected Arabidopsis mesophyll cell protoplasts. Furthermore, chromatin immunoprecipitation (ChIP) demonstrates in vivo binding of ORE1 to the BFN1 promoter. We also demonstrate binding of ORE1 in vivo to the promoters of two other senescence-associated genes, namely SAG29/SWEET15 and SINA1, supporting the central role of ORE1 during senescence.
Complex transient dynamics of stage-structured populations in response to environmental changes
(2013)
Stage structures of populations can have a profound influence on their dynamics. However, not much is known about the transient dynamics that follow a disturbance in such systems. Here we combined chemostat experiments with dynamical modeling to study the response of the phytoplankton species Chlorella vulgaris to press perturbations. From an initially stable steady state, we altered either the concentration or dilution rate of a growth-limiting resource. This disturbance induced a complex transient response-characterized by the possible onset of oscillations-before population numbers relaxed to a new steady state. Thus, cell numbers could initially change in the opposite direction of the long-term change. We present quantitative indexes to characterize the transients and to show that the dynamic response is dependent on the degree of synchronization among life stages, which itself depends on the state of the population before perturbation. That is, we show how identical future steady states can be approached via different transients depending on the initial population structure. Our experimental results are supported by a size-structured model that accounts for interplay between cell-cycle and population-level processes and that includes resource-dependent variability in cell size. Our results should be relevant to other populations with a stage structure including organisms of higher order.
Feedback inhibition of starch degradation in arabidopsis leaves mediated by trehalose 6-phosphate
(2013)
Many plants accumulate substantial starch reserves in their leaves during the day and remobilize them at night to provide carbon and energy for maintenance and growth. In this paper, we explore the role of a sugar-signaling metabolite, trehalose-6-phosphate (Tre6P), in regulating the accumulation and turnover of transitory starch in Arabidopsis (Arabidopsis thaliana) leaves. Ethanol-induced overexpression of trehalose-phosphate synthase during the day increased Tre6P levels up to 11-fold. There was a transient increase in the rate of starch accumulation in the middle of the day, but this was not linked to reductive activation of ADP-glucose pyrophosphorylase. A 2- to 3-fold increase in Tre6P during the night led to significant inhibition of starch degradation. Maltose and maltotriose did not accumulate, suggesting that Tre6P affects an early step in the pathway of starch degradation in the chloroplasts. Starch granules isolated from induced plants had a higher orthophosphate content than granules from noninduced control plants, consistent either with disruption of the phosphorylation-dephosphorylation cycle that is essential for efficient starch breakdown or with inhibition of starch hydrolysis by beta-amylase. Nonaqueous fractionation of leaves showed that Tre6P is predominantly located in the cytosol, with estimated in vivo Tre6P concentrations of 4 to 7 mu M in the cytosol, 0.2 to 0.5 mu M in the chloroplasts, and 0.05 mu M in the vacuole. It is proposed that Tre6P is a component in a signaling pathway that mediates the feedback regulation of starch breakdown by sucrose, potentially linking starch turnover to demand for sucrose by growing sink organs at night.
Individual-based models (IBMs) predict how dynamics at higher levels of biological organization emerge from individual-level processes. This makes them a particularly useful tool for ecotoxicology, where the effects of toxicants are measured at the individual level but protection goals are often aimed at the population level or higher. However, one drawback of IBMs is that they require significant effort and data to design for each species. A solution would be to develop IBMs for chemical risk assessment that are based on generic individual-level models and theory. Here we show how one generic theory, Dynamic Energy Budget (DEB) theory, can be used to extrapolate the effect of toxicants measured at the individual level to effects on population dynamics. DEB is based on first principles in bioenergetics and uses a common model structure to model all species. Parameterization for a certain species is done at the individual level and allows to predict population-level effects of toxicants for a wide range of environmental conditions and toxicant concentrations. We present the general approach, which in principle can be used for all animal species, and give an example using Daphnia magna exposed to 3,4-dichloroaniline. We conclude that our generic approach holds great potential for standardized ecological risk assessment based on ecological models. Currently, available data from standard tests can directly be used for parameterization under certain circumstances, but with limited extra effort standard tests at the individual would deliver data that could considerably improve the applicability and precision of extrapolation to the population level. Specifically, the measurement of a toxicant's effect on growth in addition to reproduction, and presenting data over time as opposed to reporting a single EC50 or dose response curve at one time point.
Individual-based models (IBMs) are increasingly used to link the dynamics of individuals to higher levels of biological organization. Still, many IBMs are data hungry, species specific, and time-consuming to develop and analyze. Many of these issues would be resolved by using general theories of individual dynamics as the basis for IBMs. While such theories have frequently been examined at the individual level, few cross-level tests exist that also try to predict population dynamics. Here we performed a cross-level test of dynamic energy budget (DEB) theory by parameterizing an individual-based model using individual-level data of the water flea, Daphnia magna, and comparing the emerging population dynamics to independent data from population experiments. We found that DEB theory successfully predicted population growth rates and peak densities but failed to capture the decline phase. Further assumptions on food-dependent mortality of juveniles were needed to capture the population dynamics after the initial population peak. The resulting model then predicted, without further calibration, characteristic switches between small-and large-amplitude cycles, which have been observed for Daphnia. We conclude that cross-level tests help detect gaps in current individual-level theories and ultimately will lead to theory development and the establishment of a generic basis for individual-based models and ecology.
In humans, the L-cysteine desulfurase NFS1 plays a crucial role in the mitochondrial iron-sulfur cluster biosynthesis and in the thiomodification of mitochondrial and cytosolic tRNAs. We have previously demonstrated that purified NFS1 is able to transfer sulfur to the C-terminal domain of MOCS3, a cytosolic protein involved in molybdenum cofactor biosynthesis and tRNA thiolation. However, no direct evidence existed so far for the interaction of NFS1 and MOCS3 in the cytosol of human cells. Here, we present direct data to show the interaction of NFS1 and MOCS3 in the cytosol of human cells using Forster resonance energy transfer and a split-EGFP system. The colocalization of NFS1 and MOCS3 in the cytosol was confirmed by immunodetection of fractionated cells and localization studies using confocal fluorescence microscopy. Purified NFS1 was used to reconstitute the lacking molybdoenzyme activity of the Neurospora crassa nit-1 mutant, giving additional evidence that NFS1 is the sulfur donor for Moco biosynthesis in eukaryotes in general.
Plants metabolize transitory starch by precisely coordinated plastidial and cytosolic processes. The latter appear to include the action of water-soluble heteroglycans (SHG(in)) whose monosaccharide pattern is similar to that of apoplastic glycans (SHG(ex)) but, unlike SHG(ex), SHG(in) strongly interacts with glucosyl transferases. In this study, we analyzed starch metabolism using mesophyll protoplasts from wild-type plants and two knock-out mutants [deficient in the cytosolic transglucosidase, disproportionating isoenzyme 2 (DPE2) or the plastidial phosphoglucomutase (PGM1)] from Arabidopsis thaliana. Protoplasts prelabeled by photosynthetic (CO2)-C-14 fixation were transferred to an unlabeled medium and were darkened or illuminated. Carbon transitions from the Calvin cycle or from starch to both SHG(in) and SHG(ex) were analyzed. In illuminated protoplasts, starch turn-over was undetectable but darkened protoplasts continuously degraded starch. During illumination, neither the total C-14 content nor the labeling patterns of the sugar residues of SHG(in) were significantly altered but both the total amount and the labeling of the constituents of SHG(ex) increased with time. In darkened protoplasts, the C-14-content of most of the sugar residues of SHG(in) transiently and strongly increased and then declined. This effect was not observed in any SHG(ex) constituent. In darkened DPE2-deficient protoplasts, none of the SHG(in) constituents exhibited an essential transient increase in labeling. In contrast, some residues of SHG(in) from the PGM1 mutant exhibited a transient increase in label but this effect significantly differed from that of the wild type. Two conclusions are reached: first, SHG(in) and SHG(ex) exert different metabolic functions and second, SHG(in) is directly involved in starch degradation.
In order to elucidate factors that determine substrate specificity and activity of mammalian molybdo-flavoproteins we performed site directed mutagenesis of mouse aldehyde oxidase 3 (mAOX3). The sequence alignment of different aldehyde oxidase (AOX) isoforms identified variations in the active site of mAOX3 in comparison to other AOX proteins and xanthine oxidoreductases (XOR). Based on the structural alignment of mAOX3 and bovine XOR, differences in amino acid residues involved in substrate binding in XORs in comparison to AOXs were identified. We exchanged several residues in the active site to the ones found in other AOX homologues in mouse or to residues present in bovine XOR in order to examine their influence on substrate selectivity and catalytic activity. Additionally we analyzed the influence of the [2Fe-2S] domains of mAOX3 on its kinetic properties and cofactor saturation. We applied UV-VIS and EPR monitored redox-titrations to determine the redox potentials of wild type mAOX3 and mAOX3 variants containing the iron-sulfur centers of mAOX1. In addition, a combination of molecular docking and molecular dynamic simulations (MD) was used to investigate factors that modulate the substrate specificity and activity of wild type and AOX variants. The successful conversion of an AOX enzyme to an XOR enzyme was achieved exchanging eight residues in the active site of mAOX3. It was observed that the absence of the K889H exchange substantially decreased the activity of the enzyme towards all substrates analyzed, revealing that this residue has an important role in catalysis.
Tyrant flycatchers (Aves: Tyrannidae) are endemic to the New World, and many species of this group are threatened or near-threatened at the global level. The aim of this study was to test the 18 microsatellite markers that have been published for other Tyrant flycatchers in the Strange-tailed Tyrant (Alectrurus risora) and the Sharp-tailed Tyrant (Culicivora caudacuta), two endemic species of southern South American grasslands that are classified as vulnerable. We also analyzed the usefulness of loci in relation to phylogenetic distance to the source species. Amplification success was high in both species (77 to 83%) and did not differ between the more closely and more distantly related species to the source species. Polymorphism success was also similar for both species, with 9 and 8 loci being polymorphic, respectively. An increased phylogenetic distance thus does not gradually lead to allelic or locus dropouts, implying that in Tyrant flycatchers, the published loci are useful independent of species relatedness.
Up to 15% of the genes in different genomes overlap. This architecture, although beneficial for the genome size, represents an obstacle for simultaneous transcription of both genes. Here we analyze the interference between RNA-polymerase II (Pol II) and RNA-polymerase III (Pol III) when transcribing their target genes encoded on opposing strands within the same DNA fragment in Arabidopsis thaliana. The expression of a Pol II-dependent protein-coding gene negatively correlated with the transcription of a Pol III-dependent, tRNA-coding gene set. We suggest that the architecture of the overlapping genes introduces an additional layer of control of gene expression. (C) 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
The neonate nutrition hypothesis - early feeding affects the body stoichiometry of Daphnia offspring
(2013)
Aquatic herbivores consume variable quantities and qualities of food. In freshwater systems, where phosphorus (P) is often a primary limiting element, inadequate dietary P can slow maternal growth and reduce body P content. There remains uncertainty about whether and how dietary effects on mothers are transferred to offspring by way of egg provisioning. Using the keystone herbivore Daphnia, we tested a novel explanation (the neonate nutrition hypothesis') to determine whether the early nutrition of newborns affects their elemental composition and whether the indications of differences in maternal P nutrition found previously might be overestimated. We thus examined the P content of mothers and their eggs from deposition through development to the birth of neonates. We examined further whether very short periods of ingestion (3h) by the offspring alter the overall P content of juvenile Daphnia. We showed that strong dietary P effects on mothers were not directly transferred to their eggs. Irrespective of the supply of P in the maternal diet, the P content of eggs in different developmental stages and in (unfed) neonates did not differ. This indicates that Daphnia mothers do not reduce the quality (in terms of P) of newly produced offspring after intermittent periods (i.e. several days) of poor nutrition. In contrast, the P content of neonates reflected that of their food after brief periods of feeding, indicating that even temporary exposure to nutrient poor food immediately after birth may strongly affect the elemental composition of neonates. Our results thus support the neonate nutrition hypothesis, which, like differential maternal provisioning, is a possible explanation for the variable elemental quality of young Daphnia.