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 cancers are created equal: Tissue specificity in cancer genes and pathways

Tumors arise through waves of genetic alterations and clonal expansion that allow tumor cells to acquire cancer hallmarks, such as genome instability and immune evasion. Recent genomic analyses showed that the vast majority of cancer driver genes are mutated in a tissue-dependent manner, that is, are altered in some cancers but not others. Often the tumor type also affects the likelihood of therapy response. What is the origin of tissue specificity in cancer? Recent studies suggest that both cell-intrinsic and cell-extrinsic factors play a role. On one hand, cell type–specific wiring of the cell signaling network determines the outcome of cancer driver gene mutations. On the other hand, the tumor cells’ exposure to tissue-specific microenvironments (e.g. immune cells) also contributes to shape the tissue specificity of driver genes and of therapy response. In the future, a more complete understanding of tissue specificity in cancer may inform methods to better predict and improve therapeutic outcomes.     

Not all sanctuaries are created equal: variation in protected area selection by wintering mallards

Public lands managed for wildlife frequently provide various forms of sanctuary to increase residency times and allow access to energetic and other habitat resources for waterfowl. The influence of sanctuary type and disturbance regime on resource use and fine-scale movements of waterfowl has not been investigated extensively using currently available transmitter technologies. We examined mallard (Anas platyrhynchos) use of various types of waterfowl sanctuary and non-sanctuary areas in the Mississippi Alluvial Valley region of eastern Arkansas, USA, during winters of 2019–2021. We deployed 105 global positioning system transmitters on mallards at 4 closed-access spatial sanctuaries on or adjacent to Dale Bumpers White River National Wildlife Refuge. We used hourly transmitter locations to examine mallard use of public sanctuary areas, public hunt areas, and private lands using integrated step selection analysis. Public sanctuary areas provided varying levels of protected status, public hunt areas allowed for varying levels of hunting intensity by duck hunters, and private lands were open to waterfowl hunting and other forms of private uses but may or may not have been hunted at any specific frequency. Mallards selected spatial sanctuary and avoided public hunt areas, other sanctuary types, and private lands during the day. In contrast, mallards selected for private lands over spatial sanctuary at night. Mallards tended to avoid areas that allowed duck hunting or used them during the night when risk of harvest mortality was removed. After the hunting season closed, mallards began using areas that previously allowed duck hunting during the day, suggesting that risk was the primary factor influencing site use. Moreover, mallards were 1.6 times more likely to use public daily hunt areas and 2.1 times more likely to use private lands potentially open to hunting during the day than spatial sanctuary 2 weeks after the close of duck hunting season in February. Spatial sanctuaries appear more effective in influencing mallard use than temporal sanctuaries or inviolate sanctuaries, which are commonly used by state and federal agencies. Partial daily, daily, or activity-specific (e.g., no hunting past noon, no hunting 3 days/week, no waterfowl hunting) closures to encourage mallard use of temporal sanctuaries do not appear to reduce the perceived harvest-related risk to mallards enough for them to view these areas as accessible or significantly increase their use.     

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 J domains are created equal: implications for the specificity of Hsp40-Hsp70 interactions

Heat shock protein 40s (Hsp40s) and heat shock protein 70s (Hsp70s) form chaperone partnerships that are key components of cellular chaperone networks involved in facilitating the correct folding of a broad range of client proteins. While the Hsp40 family of proteins is highly diverse with multiple forms occurring in any particular cell or compartment, all its members are characterized by a J domain that directs their interaction with a partner Hsp70. Specific Hsp40-Hsp70 chaperone partnerships have been identified that are dedicated to the correct folding of distinct subsets of client proteins. The elucidation of the mechanism by which these specific Hsp40-Hsp70 partnerships are formed will greatly enhance our understanding of the way in which chaperone pathways are integrated into finely regulated protein folding networks. From in silico analyses, domain swapping and rational protein engineering experiments, evidence has accumulated that indicates that J domains contain key specificity determinants. This review will critically discuss the current understanding of the structural features of J domains that determine the specificity of interaction between Hsp40 proteins and their partner Hsp70s. We also propose a model in which the J domain is able to integrate specificity and chaperone activity.     

Not all fish are equal: functional biodiversity of cartilaginous fishes (Elasmobranchii and Holocephali) in Chile

A review of the primary literature on the cartilaginous fishes (sharks, skates, rays and chimaeras), together with new information suggests that 106 species occur in Chilean waters, comprising 58 sharks, 30 skates, 13 rays and five chimaeras. The presence of 93 species was confirmed, although 30 species were encountered rarely, through validated catch records and sightings made in artisanal and commercial fisheries and on specific research cruises. Overall, only 63 species appear to have a range distribution that normally includes Chilean waters. Actual reliable records of occurrence are lacking for 13 species. Chile has a cartilaginous fish fauna that is relatively impoverished compared with the global species inventory, but conservative compared with countries in South America with warm‐temperate waters. The region of highest species richness occurs in the mid‐Chilean latitudes of c. 30–40° S. This region represents a transition zone with a mix of species related to both the warm‐temperate Peruvian province to the north and cold‐temperate Magellan province to the south. This study provides clarification of species occurrence and the functional biodiversity of Chile's cartilaginous fish fauna.     

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 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 droughts are created equal: the impacts of interannual drought pattern and magnitude on grassland carbon cycling

Climate extremes, such as drought, may have immediate and potentially prolonged effects on carbon cycling. Grasslands store approximately one‐third of all terrestrial carbon and may become carbon sources during droughts. However, the magnitude and duration of drought‐induced disruptions to the carbon cycle, as well as the mechanisms responsible, remain poorly understood. Over the next century, global climate models predict an increase in two types of drought: chronic but subtle ‘press‐droughts’, and shorter term but extreme ‘pulse‐droughts’. Much of our current understanding of the ecological impacts of drought comes from experimental rainfall manipulations. These studies have been highly valuable, but are often short term and rarely quantify carbon feedbacks. To address this knowledge gap, we used the Community Land Model 4.0 to examine the individual and interactive effects of pulse‐ and press‐droughts on carbon cycling in a mesic grassland of the US Great Plains. A series of modeling experiments were imposed by varying drought magnitude (precipitation amount) and interannual pattern (press‐ vs. pulse‐droughts) to examine the effects on carbon storage and cycling at annual to century timescales. We present three main findings. First, a single‐year pulse‐drought had immediate and prolonged effects on carbon storage due to differential sensitivities of ecosystem respiration and gross primary production. Second, short‐term pulse‐droughts caused greater carbon loss than chronic press‐droughts when total precipitation reductions over a 20‐year period were equivalent. Third, combining pulse‐ and press‐droughts had intermediate effects on carbon loss compared to the independent drought types, except at high drought levels. Overall, these results suggest that interannual drought pattern may be as important for carbon dynamics as drought magnitude and that extreme droughts may have long‐lasting carbon feedbacks in grassland ecosystems.     

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 all types of host contacts are equal when it comes to E. coli transmission

The specific processes that facilitate pathogen transmission are poorly understood, particularly for wild animal populations. A major impediment for investigating transmission pathways is the need for simultaneous information on host contacts and pathogen transfer. In this study, we used commensal Escherichia coli strains as a model system for gastrointestinal pathogens. We combined strain‐sharing information with detailed host contact data to investigate transmission routes in mountain brushtail possums. Despite E. coli being transmitted via the faecal‐oral route, we revealed that, strain‐sharing among possums was better explained by host contacts than spatial proximity. Furthermore, and unexpectedly, strain‐sharing was more strongly associated with the duration of brief nocturnal associations than day‐long den‐sharing. Thus, the most cryptic and difficult associations to measure were the most relevant connections for the transmission of this symbiont. We predict that future studies that employ similar approaches will reveal the importance of previously overlooked associations as key transmission pathways.     

Not all weeds are created equal: A database approach uncovers differences in the sexual system of native and introduced weeds

Weedy species provide excellent opportunities to examine the process of successful colonization of novel environments. Despite the influence of the sexual system on a variety of processes from reproduction to genetic structure, how the sexual system of species influences weediness has received only limited consideration. We examined the hypothesis that weedy plants have an increased likelihood of being self‐compatible compared with nonweedy plants; this hypothesis is derived from Baker's law, which states that species that can reproduce uniparentally are more likely to successfully establish in a new habitat where mates are lacking. We combined a database of the weed (weedy/nonweedy) and introduction status (introduced/native) of plant species found in the USA with a database of plant sexual systems and determined whether native and introduced weeds varied in their sexual systems compared with native and introduced nonweeds. We found that introduced weeds are overrepresented by species with both male and female functions present within a single flower (hermaphrodites) whereas weeds native to the USA are overrepresented by species with male and female flowers present on a single plant (monoecious species). Overall, our results show that Baker's law is supported at the level of the sexual system, thus providing further evidence that uniparental reproduction is an important component of being either a native or introduced weed.