Not all anthocyanins are born equal: distinct patterns induced by stress in Arabidopsis

Main Conclusion

Different abiotic stress conditions induce distinct sets of anthocyanins, indicating that anthocyanins have different biological functions, or that decoration patterns of each anthocyanin are used for unique purposes during stress. The induction of anthocyanin accumulation in vegetative tissues is often considered to be a response of plants to biotic or abiotic stress conditions. Arabidopsis thaliana (Arabidopsis) accumulates over 20 anthocyanins derived from the anthocyanidin cyanidin in an organ-specific manner during development, but the anthocyanin chemical diversity for their alleged stress protective functions remains unclear. We show here that, when grown in various abiotic stress conditions, Arabidopsis not only often accumulates significantly higher levels of total anthocyanins, but different stress conditions also favor the accumulation of different sets of anthocyanins. For example, the anthocyanin patterns of seedlings grown at pH 3.3 or in media lacking phosphate are very similar and characterized by relatively high levels of the anthocyanins A8 and A11. In contrast, anthocyanin inductive conditions (AIC) provided by high sucrose media are characterized by high accumulation of A9* and A5 relative to other stress conditions. The modifications present in each condition correlate reasonably well with the induction of the respective anthocyanin modification enzymes. Taken together, our results suggest that Arabidopsis anthocyanin profiles provide ‘fingerprints’ that reflect the stress status of the plants.     

Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

Background

Sequence homology considerations widely used to transfer functional annotation to uncharacterized protein sequences require special precautions in the case of non-globular sequence segments including membrane-spanning stretches composed of non-polar residues. Simple, quantitative criteria are desirable for identifying transmembrane helices (TMs) that must be included into or should be excluded from start sequence segments in similarity searches aimed at finding distant homologues.

Results

We found that there are two types of TMs in membrane-associated proteins. On the one hand, there are so-called simple TMs with elevated hydrophobicity, low sequence complexity and extraordinary enrichment in long aliphatic residues. They merely serve as membrane-anchoring device. In contrast, so-called complex TMs have lower hydrophobicity, higher sequence complexity and some functional residues. These TMs have additional roles besides membrane anchoring such as intra-membrane complex formation, ligand binding or a catalytic role. Simple and complex TMs can occur both in single- and multi-membrane-spanning proteins essentially in any type of topology. Whereas simple TMs have the potential to confuse searches for sequence homologues and to generate unrelated hits with seemingly convincing statistical significance, complex TMs contain essential evolutionary information.

Conclusion

For extending the homology concept onto membrane proteins, we provide a necessary quantitative criterion to distinguish simple TMs (and a sufficient criterion for complex TMs) in query sequences prior to their usage in homology searches based on assessment of hydrophobicity and sequence complexity of the TM sequence segments.

Reviewers

This article was reviewed by Shamil Sunyaev, L. Aravind and Arcady Mushegian.     

DNA double strand breaks: Not all foci are created equal

Comment on: Processing of O6-methylguanine into DNA double-strand breaks requires two rounds of replication whereas apoptosis is also induced in subsequent cell cycles. Quiros S, et al. Cell Cycle 2010; 9:In press.     

Not all secretory granules are created equal: Partitioning of soluble content proteins

Secretory granules carrying fluorescent cargo proteins are widely used to study granule biogenesis, maturation, and regulated exocytosis. We fused the soluble secretory protein peptidylglycine alpha-hydroxylating monooxygenase (PHM) to green fluorescent protein (GFP) to study granule formation. When expressed in AtT-20 or GH3 cells, the PHM-GFP fusion protein partitioned from endogenous hormone (adrenocorticotropic hormone, growth hormone) into separate secretory granule pools. Both exogenous and endogenous granule proteins were stored and released in response to secretagogue. Importantly, we found that segregation of content proteins is not an artifact of overexpression nor peculiar to GFP-tagged proteins. Neither luminal acidification nor cholesterol-rich membrane microdomains play essential roles in soluble content protein segregation. Our data suggest that intrinsic biophysical properties of cargo proteins govern their differential sorting, with segregation occurring during the process of granule maturation. Proteins that can self-aggregate are likely to partition into separate granules, which can accommodate only a few thousand copies of any content protein; proteins that lack tertiary structure are more likely to distribute homogeneously into secretory granules. Therefore, a simple "self-aggregation default" theory may explain the little acknowledged, but commonly observed, tendency for both naturally occurring and exogenous content proteins to segregate from each other into distinct secretory granules.     

Not all colors are equal: predation and color polytypism in the aposematic poison frog Oophaga pumilio

Aposematic organisms are not predicted to show high levels of warning signal diversity because they are expected to be under stabilizing selection to decrease costs of ‘educating’ predators about their unpalatability. However, systematic changes in warning signals (polytypism) can be expected if they represent adaptations to local predators. The aposematic strawberry poison frog (Oophaga pumilio) is red throughout its mainland distribution in Costa Rica and Panamá, but displays high levels of warning signal diversity in the Bocas del Toro Archipelago of Panamá. Both coloration and spot pattern vary in a polytypic sense. Sexual selection contributes to maintaining the polytypism, but little work has investigated the potential influence of predation. We used unspotted models of O. pumilio to determine if predation might help explain the color polytypism on Isla Colón in the Bocas del Toro Archipelago of Panamá. We tested whether attack rates differed among the red mainland morph, green/yellow Isla Colón morph, and the brown control. We found that frog color significantly predicted being attacked. The local green Isla Colón models were attacked more than foreign red or brown models. No difference in attack rate existed between red and brown control models. Our results suggest that the red mainland morph possesses a more effective warning signal, even when it is not the local morph. Honest signaling of unpalatability, neophobia, and the use of search images by local predators are potential explanations. Similarity of the brown model to other local poison frogs might explain the lower attack rate compared to previous work. The attack rate was lower on Isla Colón compared to mainland Costa Rica, which supports the hypothesis that less overall predation in the Bocas del Toro Archipelago may contribute to the overall warning signal diversity in O. pumilio there by relaxing selection for aposematic traits.     

Not all locations are created equal: exploring how adults hide and search for objects

Little is known about the strategies people use to effectively hide objects from others, or to search for objects others have hidden. The present research extends a recent investigation of people's hiding and searching strategies in a simple room with 9 cache location. In the present studies, people hid and searched for three objects under more than 70 floor tiles in complex real and virtual rooms. Experiment 1 replicated several finding of Talbot et al within the more complex real and virtual environments. Specifically, people traveled further from origin and selected more dispersed locations when hiding than when searching. Experiments 2 and 3 showed that: 1) people were attracted to an area of darkness when searching and avoided locations close to a window when hiding, 2) when search attempts were limited to three choices, people searched farther from origin and dispersed their locations more when hiding than when searching, and 3) informing people that they would need to recover their hidden objects altered their hiding behavior and increased recovery accuracy. Across all experiments, consistencies in location preferences emerged, with more preference for the middle of the room during hiding and more preference for corners of the room during searching. Even though the same people participated in both the hiding and searching tasks, it appears that people use different strategies to select hiding places than to search for objects hidden by others.     

Not all mice are equal: welfare implications of behavioural habituation profiles in four 129 mouse substrains

Safeguarding the welfare of animals is an important aim when defining housing and management standards in animal based, experimental research. While such standards are usually defined per animal species, it is known that considerable differences between laboratory mouse strains exist, for example with regard to their emotional traits. Following earlier experiments, in which we found that 129P3 mice show a lack of habituation of anxiety related behaviour after repeated exposure to an initially novel environment (non-adaptive profile), we here investigated four other 129 inbred mouse substrains (129S2/SvPas, 129S2/SvHsd (exp 1); 129P2 and 129X1 (exp 2)) on habituation of anxiety related behaviour. Male mice of each strain were repeatedly placed in the modified hole board test, measuring anxiety-related behaviour, exploratory and locomotor behaviour. The results reveal that all four substrains show a lack of habituation behaviour throughout the period of testing. Although not in all of the substrains a possible confounding effect of general activity can be excluded, our findings suggest that the genetic background of the 129 substrains may increase their vulnerability to cope with environmental challenges, such as exposure to novelty. This vulnerability might negatively affect the welfare of these mice under standard laboratory conditions when compared with other strains. Based on our findings we suggest to consider (sub)strain-specific guidelines and protocols, taking the (subs)train-specific adaptive capabilities into account.     

Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels

Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different to ensure sequencing, replication, and oligonucleotide synthesis errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against substitution errors during sequencing and extant tag sets contain too few tag sequences. We developed an open-source software package to validate sequence tags for conformance to two distance metrics and design sequence tags robust to indel and substitution errors. We use this software package to evaluate several commercial and non-commercial sequence tag sets, design several large sets (max_count = 7,198) of edit metric sequence tags having different lengths and degrees of error correction, and integrate a subset of these edit metric tags to polymerase chain reaction (PCR) primers and sequencing adapters. We validate a subset of these edit metric tagged PCR primers and sequencing adapters by sequencing on several platforms and subsequent comparison to commercially available alternatives. We find that several commonly used sets of sequence tags or design methodologies used to produce sequence tags do not meet the minimum expectations of their underlying distance metric, and we find that PCR primers and sequencing adapters incorporating edit metric sequence tags designed by our software package perform as well as their commercial counterparts. We suggest that researchers evaluate sequence tags prior to use or evaluate tags that they have been using. The sequence tag sets we design improve on extant sets because they are large, valid across the set, and robust to the suite of substitution, insertion, and deletion errors affecting massively parallel sequencing workflows on all currently used platforms.     

Not all isolates are equal: linkage disequilibrium analysis on Xq13.3 reveals different patterns in Sardinian sub-populations

Recent studies indicate that, whereas the Sardinian population as a whole is comparable to outbred populations for linkage disequilibrium (LD) mapping of common variants, LD in Sardinian sub-isolates is more extended, making these populations particularly suitable for this approach. To evaluate the extent of LD between microsatellite markers, we compared different sub-populations within Sardinia selected on the basis of their geographical position and isolation: two small isolated villages (Talana, Urzulei), two larger but remote areas (Ogliastra, Nuoro province) and a cohort of samples representing the wider Sardinian population. LD analysis was carried out by using six microsatellite markers that are located on Xq13.3 and that have been extensively studied in different populations. We found different extents and patterns of LD in the sub-population samples depending on their degree of isolation and demographic history. All LD measurements and haplotype analyses indicate that there is a decreasing trend from Talana (the most inbred population, LD up to 9.5-11.5 Mb) to the more outbred Sardinian population (LD only for intervals <2 Mb). In one village (Talana), five haplotype classes accounting for 80% of the entire sample perfectly matched five Ogliastra clusters, supporting the origin of the village from the Ogliastra genetic pool. In contrast, the other village (Urzulei) showed a different pattern of haplotypes with a closer relationship to the Nuoro region sub-population. LD analyses therefore show that even neighbouring isolate villages may differ in their genetic background. Here, we highlight the importance of selecting appropriate populations and/or sub-populations for the analysis of complex traits. Isolated sub-populations showing different extents of LD can provide a powerful method for mapping complex traits by LD scanning at relatively low marker density.     

Not all kinds of revegetation are created equal: revegetation type influences bird assemblages in threatened Australian woodland ecosystems

The value for biodiversity of large intact areas of native vegetation is well established. The biodiversity value of regrowth vegetation is also increasingly recognised worldwide. However, there can be different kinds of revegetation that have different origins. Are there differences in the richness and composition of biotic communities in different kinds of revegetation? The answer remains unknown or poorly known in many ecosystems. We examined the conservation value of different kinds of revegetation through a comparative study of birds in 193 sites surveyed over ten years in four growth types located in semi-cleared agricultural areas of south-eastern Australia. These growth types were resprout regrowth, seedling regrowth, plantings, and old growth.Our investigation produced several key findings: (1) Marked differences in the bird assemblages of plantings, resprout regrowth, seedling regrowth, and old growth. (2) Differences in the number of species detected significantly more often in the different growth types; 29 species for plantings, 25 for seedling regrowth, 20 for resprout regrowth, and 15 for old growth. (3) Many bird species of conservation concern were significantly more often recorded in resprout regrowth, seedling regrowth or plantings but no species of conservation concern were recorded most often in old growth. We suggest that differences in bird occurrence among different growth types are likely to be strongly associated with growth-type differences in stand structural complexity.Our findings suggest a range of vegetation growth types are likely to be required in a given farmland area to support the diverse array of bird species that have the potential to occur in Australian temperate woodland ecosystems. Our results also highlight the inherent conservation value of regrowth woodland and suggest that current policies which allow it to be cleared or thinned need to be carefully re-examined.     

Not all sperm are equal: functional mitochondria characterize a subpopulation of human sperm with better fertilization potential

Human sperm samples are very heterogeneous and include a low amount of truly functional gametes. Distinct strategies have been developed to characterize and isolate this specific subpopulation. In this study we have used fluorescence microscopy and fluorescence-activated cell sorting to determine if mitochondrial function, as assessed using mitochondrial-sensitive probes, could be employed as a criterion to obtain more functional sperm from a given ejaculate. We first determined that mitochondrial activity correlated with the quality of distinct human samples, from healthy donors to patients with decreased semen quality. Furthermore, using fluorescence-activated cell sorting to separate sperm with active and inactive mitochondria we found that this was also true within samples. Indeed, sperm with active mitochondria defined a more functional subpopulation, which contained more capacitated and acrosome intact cells, sperm with lower chromatin damage, and, crucially, sperm more able to decondense and participate in early development using both chemical induction and injection into mature bovine oocytes. Furthermore, cell sorting using mitochondrial activity produced a more functional sperm subpopulation than classic swim-up, both in terms of improvement in a variety of functional sperm parameters and in statistical significance. In conclusion, whatever the true biological role of sperm mitochondria in fertilization, mitochondrial activity is a clear hallmark of human sperm functionality.     

Not born equal: increased rate asymmetry in relocated and retrotransposed rodent gene duplicates

Duplicated genes frequently evolve at different rates. This asymmetry is evidence of natural selection's ability to discriminate between the 2 copies, subjecting them to different levels of purifying selection or even permitting adaptive evolution of one or both copies. However, if gene duplication creates pairs of protein-coding sequences that are initially identical, this raises the question of how selection tells the 2 copies apart. Here, we investigated asymmetric sequence divergence of recently duplicated genes in rodents and related this to 2 possible sources of such asymmetry: gene relocation as a consequence of duplication and retrotransposition as a mechanism of gene duplication. We found that most young rodent duplicates that have been relocated were created by retrotransposition. The degree of rate asymmetry in gene pairs where one copy has been relocated (either by retrotransposition or DNA-based duplication) is greater than in pairs formed by local DNA-based duplication events. Furthermore, by considering the direction of transposition for distant duplicates, we found a consistent tendency for retrogenes to undergo accelerated protein evolution relative to their static paralogs, whereas DNA-based transpositions showed no such tendency. Finally, we demonstrate that the faster sequence evolution of retrogenes correlates with the profound alteration of their expression pattern that is precipitated by retrotransposition.     

Not all ants are equal: obligate acacia ants provide different levels of protection against mega‐herbivores

In obligate ant–plant mutualisms, the asymmetric engagement of a single plant species with multiple ant species provides the opportunity for partners to vary in their behaviour. Variation in behaviour has implications for the interactions with third‐party species such as herbivores. This study assessed the effect of obligate ant‐mutualists (Crematogaster mimosae, Crematogaster nigriceps and Tetraponera penzigi) inhabiting the African ant‐acacia (Acacia drepanolobium) on three mega‐herbivore browsers: the Maasai giraffe (Giraffa camelopardalis tippelskirchi), the reticulated giraffe (Giraffa c. reticulata) and the black rhino (Diceros bicornis). Giraffes are abundant and wide‐ranging herbivores of the acacias, whereas black rhinos are localized and perennial herbivores of the acacias. Multiyear field studies comparing the ants’ aggressive behaviour and browsing by mega‐herbivores suggested differences between the tending abilities of the primary ant species inhabiting A. drepanolobium. Trees occupied by the aggressive ant species C. mimosae had significantly less browsing by giraffes and black rhino than trees occupied by other ant species. The results of this study provide evidence that ant‐mutualists on African acacias can serve as deterrents to mega‐herbivores and that different ant species vary in their tending abilities.     

Not all perlecans are created equal: interactions with fibroblast growth factor (FGF) 2 and FGF receptors

Human basement membrane heparan sulfate proteoglycan (HSPG) perlecan binds and activates fibroblast growth factor (FGF)-2 through its heparan sulfate (HS) chains. Here we show that perlecans immunopurified from three cellular sources possess different HS structures and subsequently different FGF-2 binding and activating capabilities. Perlecan isolated from human umbilical arterial endothelial cells (HUAEC) and a continuous endothelial cell line (C11 STH) bound similar amounts of FGF-2 either alone or complexed with FGFRalpha1-IIIc or FGFR3alpha-IIIc. Both perlecans stimulated the growth of BaF3 cell lines expressing FGFR1b/c; however, only HUAEC perlecan stimulated those cells expressing FGFR3c, suggesting that the source of perlecan confers FGF and FGFR binding specificity. Despite these differences in FGF-2 activation, the level of 2-O- and 6-O-sulfation was similar for both perlecans. Interestingly, perlecan isolated from a colon carcinoma cell line that was capable of binding FGF-2 was incapable of activating any BaF3 cell line unless the HS was removed from the protein core. The HS chains also exhibited greater bioactivity after digestion with heparinase III. Collectively, these data clearly demonstrate that the bioactivity of HS decorating a single PG is dependent on its cell source and that subtle changes in structure including secondary interactions have a profound effect on biological activity.     

Novel object exploration in mice: not all objects are created equal

Object exploration is an increasingly popular experimental paradigm in behavioral sciences. We have begun a series of studies with mice specifically looking at the parameters that influence behaviors in this test. The aim of the present study was to examine the effect of object type on performance in the object exploration test. More specifically, adult male C57BL/6J mice were trained and tested using objects that could be climbed (CLIMB) or with those that could only be touched (TOUCH). The results show that activity is affected by the presentation of objects, with object type interacting with some of these changes. C57 mice explored objects that can be climbed over significantly longer than objects that can only be touched and a more rapid habituation was observed using objects that could only be touched. Robust recognition memory was observed in both groups of mice, however mice in the CLIMB group exhibited a significantly greater discrimination index compared to mice in the TOUCH group. Taken together, these findings demonstrate that the selection of objects is of critical importance and it is recommended that special attention be given to the functional (affordant) properties of the objects to-be-used in future studies.     

Targeting mechanisms in myelinated axons: not all nodes are created equal

A recent Neuron paper by Zhang et al. (2012) reveals how ion channels and adhesion molecules essential for rapid nerve conduction in vertebrates are differentially targeted to nodes of Ranvier. Moreover, distinct mechanisms regulate initial clustering and maintenance of specific nodal components.     

Programmed genome rearrangements: in lampreys, all cells are not equal

How can organisms silence deleterious gene loci? A recent study has shed light on a very brute mechanism in a jawless vertebrate: the irreversible deletion of massive chunks of genomic DNA.     

On the evolution of scale-free topologies with a gene regulatory network model

A novel approach to generating scale-free network topologies is introduced, based on an existing artificial gene regulatory network model. From this model, different interaction networks can be extracted, based on an activation threshold. By using an evolutionary computation approach, the model is allowed to evolve, in order to reach specific network statistical measures. The results obtained show that, when the model uses a duplication and divergence initialisation, such as seen in nature, the resulting regulation networks not only are closer in topology to scale-free networks, but also require only a few evolutionary cycles to achieve a satisfactory error value.