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Wind influences the development, architecture and morphology of plant roots and may modify subsequent interactions between plants and soil (plant–soil feedbacks—PSFs). However, information on wind effects on fine root morphology is scarce and the extent to which wind changes plant–soil interactions remains unclear. Therefore, we investigated the effects of two wind intensity levels by manipulating surrounding vegetation height in a grassland PSF field experiment. We grew four common plant species (two grasses and two non-leguminous forbs) with soil biota either previously conditioned by these or other species and tested the effect of wind on root:shoot ratio, fine root morphological traits as well as the outcome for PSFs. Wind intensity did not affect biomass allocation (i.e. root:shoot ratio) in any species. However, fine-root morphology of all species changed under high wind intensity. High wind intensity increased specific root length and surface area and decreased root tissue density, especially in the two grasses. Similarly, the direction of PSFs changed under high wind intensity in all four species, but differences in biomass production on the different soils between high and low wind intensity were marginal and most pronounced when comparing grasses with forbs. Because soils did not differ in plant-available nor total nutrient content, the results suggest that wind-induced changes in root morphology have the potential to influence plant–soil interactions. Linking wind-induced changes in fine-root morphology to effects on PSF improves our understanding of plant–soil interactions under changing environmental conditions.
Wind influences the development, architecture and morphology of plant roots and may modify subsequent interactions between plants and soil (plant–soil feedbacks—PSFs). However, information on wind effects on fine root morphology is scarce and the extent to which wind changes plant–soil interactions remains unclear. Therefore, we investigated the effects of two wind intensity levels by manipulating surrounding vegetation height in a grassland PSF field experiment. We grew four common plant species (two grasses and two non-leguminous forbs) with soil biota either previously conditioned by these or other species and tested the effect of wind on root:shoot ratio, fine root morphological traits as well as the outcome for PSFs. Wind intensity did not affect biomass allocation (i.e. root:shoot ratio) in any species. However, fine-root morphology of all species changed under high wind intensity. High wind intensity increased specific root length and surface area and decreased root tissue density, especially in the two grasses. Similarly, the direction of PSFs changed under high wind intensity in all four species, but differences in biomass production on the different soils between high and low wind intensity were marginal and most pronounced when comparing grasses with forbs. Because soils did not differ in plant-available nor total nutrient content, the results suggest that wind-induced changes in root morphology have the potential to influence plant–soil interactions. Linking wind-induced changes in fine-root morphology to effects on PSF improves our understanding of plant–soil interactions under changing environmental conditions.
What Colin Reynolds could tell us about nutrient limitation, N:P ratios and eutrophication control
(2020)
Colin Reynolds exquisitely consolidated our understanding of driving forces shaping phytoplankton communities and those setting the upper limit to biomass yield, with limitation typically shifting from light in winter to phosphorus in spring. Nonetheless, co-limitation is frequently postulated from enhanced growth responses to enrichments with both N and P or from N:P ranging around the Redfield ratio, concluding a need to reduce both N and P in order to mitigate eutrophication. Here, we review the current understanding of limitation through N and P and of co-limitation. We conclude that Reynolds is still correct: (i) Liebig's law of the minimum holds and reducing P is sufficient, provided concentrations achieved are low enough; (ii) analyses of nutrient limitation need to exclude evidently non-limiting situations, i.e. where soluble P exceeds 3-10 mu g/l, dissolved N exceeds 100-130 mu g/l and total P and N support high biomass levels with self-shading causing light limitation; (iii) additionally decreasing N to limiting concentrations may be useful in specific situations (e.g. shallow waterbodies with high internal P and pronounced denitrification); (iv) management decisions require local, situation-specific assessments. The value of research on stoichiometry and co-limitation lies in promoting our understanding of phytoplankton ecophysiology and community ecology.
What Colin Reynolds could tell us about nutrient limitation, N:P ratios and eutrophication control
(2020)
Colin Reynolds exquisitely consolidated our understanding of driving forces shaping phytoplankton communities and those setting the upper limit to biomass yield, with limitation typically shifting from light in winter to phosphorus in spring. Nonetheless, co-limitation is frequently postulated from enhanced growth responses to enrichments with both N and P or from N:P ranging around the Redfield ratio, concluding a need to reduce both N and P in order to mitigate eutrophication. Here, we review the current understanding of limitation through N and P and of co-limitation. We conclude that Reynolds is still correct: (i) Liebig's law of the minimum holds and reducing P is sufficient, provided concentrations achieved are low enough; (ii) analyses of nutrient limitation need to exclude evidently non-limiting situations, i.e. where soluble P exceeds 3-10 mu g/l, dissolved N exceeds 100-130 mu g/l and total P and N support high biomass levels with self-shading causing light limitation; (iii) additionally decreasing N to limiting concentrations may be useful in specific situations (e.g. shallow waterbodies with high internal P and pronounced denitrification); (iv) management decisions require local, situation-specific assessments. The value of research on stoichiometry and co-limitation lies in promoting our understanding of phytoplankton ecophysiology and community ecology.
Using individual-based modeling to understand grassland diversity and resilience in the Anthropocene
(2020)
The world’s grassland systems are increasingly threatened by anthropogenic change. Susceptible to a variety of different stressors, from land-use intensification to climate change, understanding the mechanisms driving the maintenance of these systems’ biodiversity and stability, and how these mechanisms may shift under human-mediated disturbance, is thus critical for successfully navigating the next century. Within this dissertation, I use an individual-based and spatially-explicit model of grassland community assembly (IBC-grass) to examine several processes, thought key to understanding their biodiversity and stability and how it changes under stress. In the first chapter of my thesis, I examine the conditions under which intraspecific trait variation influences the diversity of simulated grassland communities. In the second and third chapters of my thesis, I shift focus towards understanding how belowground herbivores influence the stability of these grassland systems to either a disturbance that results in increased, stochastic, plant mortality, or eutrophication.
Intraspecific trait variation (ITV), or variation in trait values between individuals of the same species, is fundamental to the structure of ecological communities. However, because it has historically been difficult to incorporate into theoretical and statistical models, it has remained largely overlooked in community-level analyses. This reality is quickly shifting, however, as a consensus of research suggests that it may compose a sizeable proportion of the total variation within an ecological community and that it may play a critical role in determining if species coexist. Despite this increasing awareness that ITV matters, there is little consensus of the magnitude and direction of its influence. Therefore, to better understand how ITV changes the assembly of grassland communities, in the first chapter of my thesis, I incorporate it into an established, individual-based grassland community model, simulating both pairwise invasion experiments as well as the assembly of communities with varying initial diversities. By varying the amount of ITV in these species’ functional traits, I examine the magnitude and direction of ITV’s influence on pairwise invasibility and community coexistence. During pairwise invasion, ITV enables the weakest species to more frequently invade the competitively superior species, however, this influence does not generally scale to the community level. Indeed, unless the community has low alpha- and beta- diversity, there will be little effect of ITV in bolstering diversity. In these situations, since the trait axis is sparsely filled, the competitively inferior may suffer less competition and therefore ITV may buffer the persistence and abundance of these species for some time.
In the second and third chapters of my thesis, I model how one of the most ubiquitous trophic interactions within grasslands, herbivory belowground, influences their diversity and stability. Until recently, the fundamental difficulty in studying a process within the soil has left belowground herbivory “out of sight, out of mind.” This dilemma presents an opportunity for simulation models to explore how this understudied process may alter community dynamics. In the second chapter of my thesis, I implement belowground herbivory – represented by the weekly removal of plant biomass – into IBC-grass. Then, by introducing a pulse disturbance, modelled as the stochastic mortality of some percentage of the plant community, I observe how the presence of belowground herbivores influences the resistance and recovery of Shannon diversity in these communities. I find that high resource, low diversity, communities are significantly more destabilized by the presence of belowground herbivores after disturbance. Depending on the timing of the disturbance and whether the grassland’s seed bank persists for more than one season, the impact of the disturbance – and subsequently the influence of the herbivores – can be greatly reduced. However, because human-mediated eutrophication increases the amount of resources in the soil, thus pressuring grassland systems, our results suggest that the influence of these herbivores may become more important over time.
In the third chapter of my thesis, I delve further into understanding the mechanistic underpinnings of belowground herbivores on the diversity of grasslands by replicating an empirical mesocosm experiment that crosses the presence of herbivores above- and below-ground with eutrophication. I show that while aboveground herbivory, as predicted by theory and frequently observed in experiments, mitigates the impact of eutrophication on species diversity, belowground herbivores counterintuitively reduce biodiversity. Indeed, this influence positively interacts with the eutrophication process, amplifying its negative impact on diversity. I discovered the mechanism underlying this surprising pattern to be that, as the herbivores consume roots, they increase the proportion of root resources to root biomass. Because root competition is often symmetric, herbivory fails to mitigate any asymmetries in the plants’ competitive dynamics. However, since the remaining roots have more abundant access to resources, the plants’ competition shifts aboveground, towards asymmetric competition for light. This leads the community towards a low-diversity state, composed of mostly high-performance, large plant species. We further argue that this pattern will emerge unless the plants’ root competition is asymmetric, in which case, like its counterpart aboveground, belowground herbivory may buffer diversity by reducing this asymmetry between the competitively superior and inferior plants.
I conclude my dissertation by discussing the implications of my research on the state of the art in intraspecific trait variation and belowground herbivory, with emphasis on the necessity of more diverse theory development in the study of these fundamental interactions. My results suggest that the influence of these processes on the biodiversity and stability of grassland systems is underappreciated and multidimensional, and must be thoroughly explored if researchers wish to predict how the world’s grasslands will respond to anthropogenic change. Further, should researchers myopically focus on understanding central ecological interactions through only mathematically tractable analyses, they may miss entire suites of potential coexistence mechanisms that can increase the coviability of species, potentially leading to coexistence over ecologically-significant timespans. Individual-based modelling, therefore, with its focus on individual interactions, will prove a critical tool in the coming decades for understanding how local interactions scale to larger contexts, and how these interactions shape ecological communities and further predicting how these systems will change under human-mediated stress.
Trends in growth and developmental tempo in boys aged 7 to 18 years between 1966 and 2012 in Poland
(2020)
Objectives:
To assess trends in growth in different developmental periods and trends in developmental tempo in Polish boys between 1966 and 2012.
Methods:
Data on 34 828 boys aged 7 to 18 years were collected during Polish Anthropological Surveys conducted in 1966, 1978, 1988, and 2012. Biological parameters, related to onset of adolescent growth spurt (OGS) and peak height velocity (PHV), were derived from a Preece-Baines 1 model (PB1). Childhood (height at 7 years of age), pre-adolescent (height at OGS) and adolescent growth (adult height minus height at OGS) were identified.
Results:
Positive secular trend between 1966 and 2012 in adult height accounted for, on average, 1.5 cm/decade, with varying intensity between the Surveys. Decline in both age at OGS and APHV between 1966 and 2012 (1.5 and 1.4 years, respectively) indicated an acceleration in developmental tempo, on average, by 0.3 year/decade. Increases in the contribution to the trend in adult height gained during growth in particular developmental periods between 1966 and 2012 were as followed-childhood: 0.6%, pre-adolescent growth: -3.1%, adolescent growth: 3.1%.
Conclusions:
Secular trend in developmental tempo and growth among boys reflects changes in living conditions and socio-political aspirations in Poland during nearly 50 years. Acceleration in tempo is already visible at age at OGS, whereas the trend in adult height occurs largely during adolescence, pointing to different regulation of developmental tempo and growth in body height. This finding emphasizes the importance of extending public health intervention into children's growth up until adolescence.
Life history theory predicts that experiencing stress during the early period of life will result in accelerated growth and earlier maturation. Indeed, animal and some human studies documented a faster pace of growth in the offspring of stressed mothers. Recent advances in epigenetics suggest that the effects of early developmental stress might be passed across the generations. However, evidence for such intergenerational transmission is scarce, at least in humans. Here we report the results of the study investigating the association between childhood trauma in mothers and physical growth in their children during the first months of life. Anthropometric and psychological data were collected from 99 mothers and their exclusively breastfed children at the age of 5 months. The mothers completed the Early Life Stress Questionnaire to assess childhood trauma. The questionnaire includes questions about the most traumatic events that they had experienced before the age of 12 years. Infant growth was evaluated based on the anthropometric measurements of weight, length, and head circumference. Also, to control for the size of maternal investment, the composition of breast milk samples taken at the time of infant anthropometric measurements was investigated. The children of mothers with higher early life stress tended to have higher weight and bigger head circumference. The association between infant anthropometrics and early maternal stress was not affected by breast milk composition, suggesting that the effect of maternal stress on infant growth was independent of the size of maternal investment. Our results demonstrate that early maternal trauma may affect the pace of growth in the offspring and, in consequence, lead to a faster life history strategy. This effect might be explained via changes in offspring epigenetics.
African weakly electric fish of the mormyrid genus Campylomormyrus generate pulse-type electric organ discharges (EODs) for orientation and communication. Their pulse durations are species-specific and elongated EODs are a derived trait. So far, differential gene expression among tissue-specific transcriptomes across species with different pulses and point mutations in single ion channel genes indicate a relation of pulse duration and electrocyte geometry/excitability. However, a comprehensive assessment of expressed Single Nucleotide Polymorphisms (SNPs) throughout the entire transcriptome of African weakly electric fish, with the potential to identify further genes influencing EOD duration, is still lacking. This is of particular value, as discharge duration is likely based on multiple cellular mechanisms and various genes. Here we provide the first transcriptome-wide SNP analysis of African weakly electric fish species (genus Campylomormyrus) differing by EOD duration to identify candidate genes and cellular mechanisms potentially involved in the determination of an elongated discharge of C. tshokwe. Non-synonymous substitutions specific to C. tshokwe were found in 27 candidate genes with inferred positive selection among Campylomormyrus species. These candidate genes had mainly functions linked to transcriptional regulation, cell proliferation and cell differentiation. Further, by comparing gene annotations between C. compressirostris (ancestral short EOD) and C. tshokwe (derived elongated EOD), we identified 27 GO terms and 2 KEGG pathway categories for which C. tshokwe significantly more frequently exhibited a species-specific expressed substitution than C. compressirostris. The results indicate that transcriptional regulation as well cell proliferation and differentiation take part in the determination of elongated pulse durations in C. tshokwe. Those cellular processes are pivotal for tissue morphogenesis and might determine the shape of electric organs supporting the observed correlation between electrocyte geometry/tissue structure and discharge duration. The inferred expressed SNPs and their functional implications are a valuable resource for future investigations on EOD durations.
External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 degrees C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes.
External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 degrees C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes.
Formaldehyde (HCHO) is a reactive carbonyl compound that formylates and cross-links proteins, DNA, and small molecules. It is of specific concern as a toxic intermediate in the design of engineered pathways involving methanol oxidation or formate reduction. The interest in engineering these pathways is not, however, matched by engineering-relevant information on precisely why HCHO is toxic or on what damage-control mechanisms cells deploy to manage HCHO toxicity. The only well-defined mechanism for managing HCHO toxicity is formaldehyde dehydrogenase-mediated oxidation to formate, which is counterproductive if HCHO is a desired pathway intermediate. We therefore sought alternative HCHO damage-control mechanisms via comparative genomic analysis. This analysis associated homologs of the Escherichia coli pepP gene with HCHO-related one-carbon metabolism. Furthermore, deleting pepP increased the sensitivity of E. coli to supplied HCHO but not other carbonyl compounds. PepP is a proline aminopeptidase that cleaves peptides of the general formula X-Pro-Y, yielding X + Pro-Y. HCHO is known to react spontaneously with cysteine to form the close proline analog thioproline (thiazolidine-4-carboxylate), which is incorporated into proteins and hence into proteolytic peptides. We therefore hypothesized that certain thioproline-containing peptides are toxic and that PepP cleaves these aberrant peptides. Supporting this hypothesis, PepP cleaved the model peptide Ala-thioproline-Ala as efficiently as Ala-Pro-Ala in vitro and in vivo, and deleting pepP increased sensitivity to supplied thioproline. Our data thus (i) provide biochemical genetic evidence that thioproline formation contributes substantially to HCHO toxicity and (ii) make PepP a candidate damage-control enzyme for engineered pathways having HCHO as an intermediate.
As the Arctic coast erodes, it drains thermokarst lakes, transforming them into lagoons, and, eventually, integrates them into subsea permafrost. Lagoons represent the first stage of a thermokarst lake transition to a marine setting and possibly more saline and colder upper boundary conditions. In this research, borehole data, electrical resistivity surveying, and modeling of heat and salt diffusion were carried out at Polar Fox Lagoon on the Bykovsky Peninsula, Siberia. Polar Fox Lagoon is a seasonally isolated water body connected to Tiksi Bay through a channel, leading to hypersaline waters under the ice cover. The boreholes in the center of the lagoon revealed floating ice and a saline cryotic bed underlain by a saline cryotic talik, a thin ice-bearing permafrost layer, and unfrozen ground. The bathymetry showed that most of the lagoon had bedfast ice in spring. In bedfast ice areas, the electrical resistivity profiles suggested that an unfrozen saline layer was underlain by a thick layer of refrozen talik. The modeling showed that thermokarst lake taliks can refreeze when submerged in saltwater with mean annual bottom water temperatures below or slightly above 0 degrees C. This occurs, because the top-down chemical degradation of newly formed ice-bearing permafrost is slower than the refreezing of the talik. Hence, lagoons may precondition taliks with a layer of ice-bearing permafrost before encroachment by the sea, and this frozen layer may act as a cap on gas migration out of the underlying talik.
The smell of hunger
(2020)
When individuals exchange helpful acts reciprocally, increasing the benefit of the receiver can enhance its propensity to return a favour, as pay-offs are typically correlated in iterated interactions. Therefore, reciprocally cooperating animals should consider the relative benefit for the receiver when deciding to help a conspecific. Norway rats (Rattus norvegicus) exchange food reciprocally and thereby take into account both the cost of helping and the potential benefit to the receiver. By using a variant of the sequential iterated prisoner's dilemma paradigm, we show that rats may determine the need of another individual by olfactory cues alone. In an experimental food-exchange task, test subjects were provided with odour cues from hungry or satiated conspecifics located in a different room. Our results show that wild-type Norway rats provide help to a stooge quicker when they receive odour cues from a hungry rather than from a satiated conspecific. Using chemical analysis by gas chromatography-mass spectrometry (GC-MS), we identify seven volatile organic compounds that differ in their abundance between hungry and satiated rats. Combined, this "smell of hunger" can apparently serve as a reliable cue of need in reciprocal cooperation, which supports the hypothesis of honest signalling.
The shape of a defense-growth trade-off governs seasonal trait dynamics in natural phytoplankton
(2020)
Theory predicts that trade-offs, quantifying costs of functional trait adjustments, crucially affect community trait adaptation to altered environmental conditions, but empirical verification is scarce. We evaluated trait dynamics (antipredator defense, maximum growth rate, and phosphate affinity) of a lake phytoplankton community in a seasonally changing environment, using literature trait data and 21 years of species-resolved high-frequency biomass measurements. The trait data indicated a concave defense-growth trade-off, promoting fast-growing species with intermediate defense. With seasonally increasing grazing pressure, the community shifted toward higher defense levels at the cost of lower growth rates along the trade-off curve, while phosphate affinity explained some deviations from it. We discuss how low fitness differences of species, inferred from model simulations, in concert with stabilizing mechanisms, e.g., arising from further trait dimensions, may lead to the observed phytoplankton diversity. In conclusion, quantifying trade-offs is key for predictions of community trait adaptation and biodiversity under environmental change.
The shape of a defense-growth trade-off governs seasonal trait dynamics in natural phytoplankton
(2020)
Theory predicts that trade-offs, quantifying costs of functional trait adjustments, crucially affect community trait adaptation to altered environmental conditions, but empirical verification is scarce. We evaluated trait dynamics (antipredator defense, maximum growth rate, and phosphate affinity) of a lake phytoplankton community in a seasonally changing environment, using literature trait data and 21 years of species-resolved high-frequency biomass measurements. The trait data indicated a concave defense-growth trade-off, promoting fast-growing species with intermediate defense. With seasonally increasing grazing pressure, the community shifted toward higher defense levels at the cost of lower growth rates along the trade-off curve, while phosphate affinity explained some deviations from it. We discuss how low fitness differences of species, inferred from model simulations, in concert with stabilizing mechanisms, e.g., arising from further trait dimensions, may lead to the observed phytoplankton diversity. In conclusion, quantifying trade-offs is key for predictions of community trait adaptation and biodiversity under environmental change.
1. We generally assume that animals should maximize information acquisition about their environment to make prudent decisions. But this is a naive assumption, as gaining information typically involves costs. <br /> 2. This is especially so in the social context, where interests between interacting partners usually diverge. The arms race involved in mutual assessment is characterized by the attempt to obtain revealing information from a partner while providing only as much information by oneself as is conducive to one's own intentions. <br /> 3. If obtaining information occasions costs in terms of time, energy and risk, animals should be selected to base their decisions on a cost-benefit ratio that takes account of the trade-off between the risk of making wrong choices and the costs involved in information acquisition, processing and use. <br /> 4. In addition, there may be physiological and/or environmental constraints limiting the ability to obtaining, processing and utilizing reliable information. <br /> 5. Here, we discuss recent empirical evidence for the proposition that social decisions are to an important extent based on the costs that result from acquiring, processing, evaluating and storing information. Using examples from different taxa and ecological contexts, we aim at drawing attention to the often neglected costs of information recipience, with emphasis on the potential role of sensory ecology and cognition in social decisions.
Iron-sulfur (Fe-S) clusters are essential protein cofactors. In enzymes, they are present either in the rhombic [2Fe-2S] or the cubic [4Fe-4S] form, where they are involved in catalysis and electron transfer and in the biosynthesis of metal-containing prosthetic groups like the molybdenum cofactor (Moco). Here, we give an overview of the assembly of Fe-S clusters in bacteria and humans and present their connection to the Moco biosynthesis pathway. In all organisms, Fe-S cluster assembly starts with the abstraction of sulfur froml-cysteine and its transfer to a scaffold protein. After formation, Fe-S clusters are transferred to carrier proteins that insert them into recipient apo-proteins. In eukaryotes like humans and plants, Fe-S cluster assembly takes place both in mitochondria and in the cytosol. Both Moco biosynthesis and Fe-S cluster assembly are highly conserved among all kingdoms of life. Moco is a tricyclic pterin compound with molybdenum coordinated through its unique dithiolene group. Moco biosynthesis begins in the mitochondria in a Fe-S cluster dependent step involving radical/S-adenosylmethionine (SAM) chemistry. An intermediate is transferred to the cytosol where the dithiolene group is formed, to which molybdenum is finally added. Further connections between Fe-S cluster assembly and Moco biosynthesis are discussed in detail.
The aim of this study was to assess the ability of the FFQ to describe reliable and valid dietary pattern (DP) scores. In a total of 134 participants of the European Prospective Investigation into Cancer and Nutrition-Potsdam study aged 35-67 years, the FFQ was applied twice (baseline and after 1 year) to assess its reliability. Between November 1995 and March 1997, twelve 24-h dietary recalls (24HDR) as reference instrument were applied to assess the validity of the FFQ. Exploratory DP were derived by principal component analyses. Investigated predefined DP were the Alternative Healthy Eating Index (AHEI) and two Mediterranean diet indices. From dietary data of each FFQ, two exploratory DP were retained, but differed in highly loading food groups, resulting in moderate correlations (r 0 center dot 45-0 center dot 58). The predefined indices showed higher correlations between the FFQ (r(AHEI) 0 center dot 62, r(Mediterranean Diet Pyramid Index (MedPyr)) 0 center dot 62 and r(traditional Mediterranean Diet Score (tMDS)) 0 center dot 51). From 24HDR dietary data, one exploratory DP retained differed in composition to the first FFQ-based DP, but showed similarities to the second DP, reflected by a good correlation (r 0 center dot 70). The predefined DP correlated moderately (r 0 center dot 40-0 center dot 60). To conclude, long-term analyses on exploratory DP should be interpreted with caution, due to only moderate reliability. The validity differed extensively for the two exploratory DP. The investigated predefined DP showed a better reliability and a moderate validity, comparable to other studies. Within the two Mediterranean diet indices, the MedPyr performed better than the tMDs in this middle-aged, semi-urban German study population.
Plants are an attractive platform for the production of medicinal compounds because of their potential to generate large amounts of biomass cheaply. The use of chloroplast transformation is an attractive way to achieve the recombinant production of proteins in plants, because of the chloroplasts’ high capacity to produce foreign proteins in comparison to nuclear transformed plants. In this thesis, the production of two different types of antimicrobial polypeptides in chloroplasts is explored.
The first example is the production of the potent HIV entry inhibitor griffithsin. Griffithsin has the potential to prevent HIV infections by blocking the entry of the virus into human cells. Here the use of transplastomic plants as an inexpensive production method for griffithsin was explored. Transplastomic plants grew healthily and were able to accumulate griffithsin to up to 5% of the total soluble protein. Griffithsin could easily be purified from tobacco leaf tissue and had a similarly high neutralization activity as griffithsin recombinantly produced in bacteria. Griffithsin could be purified from dried tobacco leaves, demonstrating that dried leaves could be used as a storable starting material for griffithsin purification, circumventing the need for immediate purification after harvest.
The second example is the production of antimicrobial peptides (AMPs) that have the capacity to kill bacteria and are an attractive alternative to currently used antibiotics that are increasingly becoming ineffective. The production of antimicrobial peptides was considerably more challenging than the production of griffithsin. Small AMPs are prone to degradation in plastids. This problem was overcome by fusing AMPs to generate larger polypeptides. In one approach, AMPs were fused to each other to increase size and combine the mode of action of multiple AMPs. This improved the accumulation of AMPs but also resulted in impaired plant growth. This was solved by the use of two different inducible systems, which could largely restore plant growth. Fusions of multiple AMPs were insoluble and could not be purified.
In addition to fusing AMPs to each other, the fusion of AMPs to small ubiquitin-like modifier (SUMO), was tested as an approach to improve the accumulation, facilitate purification, and reduce the toxicity of AMPs to chloroplasts. Fusion of AMPs to SUMO indeed increased accumulation while reducing the toxicity to the plants. SUMO fusions produced inside chloroplasts could be purified, and SUMO could be efficiently cleaved off with the SUMO protease. Such fusions therefore provide a promising strategy for the production of AMPs and other small polypeptides inside chloroplasts.
Aim: We aimed to examine the distribution and secular changes of conscript body height in the geographic network of Norway since 1878 and to study its association with the degree of urbanization, and population density. Material and methods: Data on body height of Norwegian military conscripts were provided by the Statistics Norway Department (SSB). The sample comprised eight cohorts with the following measurement years: 1st 1877, 1878 and 1880, 2nd 18951897, 3rd 1915-1917, 4th 1935-1937, 5th 1955-1957, 6th 1975-1977, 7th 1995-1997, and 8th 2009-2011. For determining neighborhood correlations, a network was created consisting of neighboring counties, sharing a common border. Results: Average body height of Norwegian men increased by 10.9 cm between 1878 and 2010, but this trend was heterogeneous. Some counties increased by more than 1 cm per decade (Finmark) others by only 7 mm per decade (Sor-Trondelag). Urban counties and counties with higher population density showed stronger height trends than rural counties. The largest spread in body height between the various counties was observed in 1936 when for the first time people living in the more urban counties got taller than rural people. The height advantage of urban counties however, disappeared after 1996. At this time, also the secular trend in height had come to a halt. The secular trend in height had become obvious after the dissolution of the union between Norway and Sweden in 1905 and World War I, and was strongest between 1936 and 1956. During this period maximum between-county heterogeneity in height existed with body height differences of more than 6 cm between the tallest and the shortest county. The end of this period was characterized by social democratic reforms that flattened the income distribution, eliminated poverty, and ensured social services after World War II. Conclusion: The temporal coincidence between the trends in height, the degree of urbanization and the onset of the political transition of Norway from a Swedish province into an independent democratic wealthy modern European state after World War I and particularly after World War II, and the abatement of this trend after this period of transition had stabilized, suggest social and political components interfering with the regulation of physical growth in humans.
The complete mitochondrial genome of oil palm pollinating weevil, Elaeidobius kamerunicus Faust
(2020)
Elaeidobius kamerunicusis the most important insect pollinator in oil palm plantations. In this study, the mitochondrial genome (mitogenome) ofE. kamerunicus(17.729 bp), a member of the Curculionidae family, will be reported. The mitogenome consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a putative control region (CR). Phylogenetic analysis based on 13 protein-coding genes (PCGs) using maximum Likelihood (ML) methods indicated thatE. kamerunicusbelongs to the Curculionidae family. This mitochondrial genome provides essential information for understanding genetic populations, phylogenetics, molecular evolution, and other biological applications in this species.
Background:
Many felid species are of high conservation concern, and with increasing human disturbance the situation is worsening. Small isolated populations are at risk of genetic impoverishment decreasing within-species biodiversity. Movement is known to be a key behavioural trait that shapes both demographic and genetic dynamics and affects population survival. However, we have limited knowledge on how different manifestations of movement behaviour translate to population processes. In this study, we aimed to 1) understand the potential effects of movement behaviour on the genetic diversity of small felid populations in heterogeneous landscapes, while 2) presenting a simulation tool that can help inform conservation practitioners following, or considering, population management actions targeting the risk of genetic impoverishment.
Methods:
We developed a spatially explicit individual-based population model including neutral genetic markers for felids and applied this to the example of Eurasian lynx. Using a neutral landscape approach, we simulated reintroductions into a three-patch system, comprising two breeding patches separated by a larger patch of differing landscape heterogeneity, and tested for the effects of various behavioural movement syndromes and founder population sizes. We explored a range of movement syndromes by simulating populations with various movement model parametrisations that range from 'shy' to 'bold' movement behaviour.
Results:
We find that movement syndromes can lead to a higher loss of genetic diversity and an increase in between population genetic structure for both "bold" and "shy" movement behaviours, depending on landscape conditions, with larger decreases in genetic diversity and larger increases in genetic differentiation associated with bold movement syndromes, where the first colonisers quickly reproduce and subsequently dominate the gene pool. In addition, we underline the fact that a larger founder population can offset the genetic losses associated with subpopulation isolation and gene pool dominance. Conclusions We identified a movement syndrome trade-off for population genetic variation, whereby bold-explorers could be saviours - by connecting populations and promoting panmixia, or sinks - by increasing genetic losses via a 'founder takes all' effect, whereas shy-stayers maintain a more gradual genetic drift due to their more cautious behaviour. Simulations should incorporate movement behaviour to provide better projections of long-term population viability and within-species biodiversity, which includes genetic diversity. Simulations incorporating demographics and genetics have great potential for informing conservation management actions, such as population reintroductions or reinforcements. Here, we present such a simulation tool for solitary felids.
The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes containing Moco, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into four steps in in bacteria: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5 '-GTP, (ii) in the second step the two sulfur atoms are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into MPT to form Moco and (iv) in the fourth step bis-Mo-MPT is formed and an additional modification of Moco is possible with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review presents an update on the well-characterized Moco biosynthesis in the model organism Escherichia coli including novel discoveries from the recent years.
The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes containing Moco, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into four steps in in bacteria: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5 '-GTP, (ii) in the second step the two sulfur atoms are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into MPT to form Moco and (iv) in the fourth step bis-Mo-MPT is formed and an additional modification of Moco is possible with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review presents an update on the well-characterized Moco biosynthesis in the model organism Escherichia coli including novel discoveries from the recent years.
Marine sponges host highly diverse but specific bacterial communities that provide essential functions for the sponge holobiont, including antimicrobial defense. Here, we characterized the bacterial microbiome of the marine sponge Haliclona cnidata that has been in culture in an artificial marine aquarium system. We tested the hypotheses (1) that the long-term aquarium cultured sponge H. cnidata is tightly associated with a typical sponge bacterial microbiota and (2) that the symbiotic Bacteria sustain bioactivity under harmful environmental conditions to facilitate holobiont survival by preventing pathogen invasion. Microscopic and phylogenetic analyses of the bacterial microbiota revealed that H. cnidata represents a high microbial abundance (HMA) sponge with a temporally stable bacterial community that significantly shifts with changing aquarium conditions. A 4-week incubation experiment was performed in small closed aquarium systems with antibiotic and/or light exclusion treatments to reduce the total bacterial and photosynthetically active sponge-associated microbiota to a treatment-specific resilient community. While the holobiont was severely affected by the experimental treatment (i.e., bleaching of the sponge, reduced bacterial abundance, shifted bacterial community composition), the biological defense and bacterial community interactions (i.e., quorum sensing activity) remained intact. 16S rRNA gene amplicon sequencing revealed a resilient community of 105 bacterial taxa, which remained in the treated sponges. These 105 taxa accounted for a relative abundance of 72-83% of the bacterial sponge microbiota of non-treated sponge fragments that have been cultured under the same conditions. We conclude that a sponge-specific resilient community stays biologically active under harmful environmental conditions, facilitating the resilience of the holobiont. In H. cnidata, bacteria are located in bacteriocytes, which may have contributed to the observed phenomenon.
When running a lab we do not think about calamities, since they are rare events for which we cannot plan while we are busy with the day-to-day management and intellectual challenges of a research lab. No lab team can be prepared for something like a pandemic such as COVID-19, which has led to shuttered labs around the globe. But many other types of crises can also arise that labs may have to weather during their lifetime. What can researchers do to make a lab more resilient in the face of such exterior forces? What systems or behaviors could we adjust in 'normal' times that promote lab success, and increase the chances that the lab will stay on its trajectory? We offer 10 rules, based on our current experiences as a lab group adapting to crisis.
Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species’ adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.
Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species’ adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.
Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.
Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.
With populations growing worldwide and climate change threatening food production there is an urgent need to find ways to ensure food security. Increasing carbon fixation rate in plants is a promising approach to boost crop yields. The carbon-fixing enzyme Rubisco catalyzes, beside the carboxylation reaction, also an oxygenation reaction that generates glycolate-2P, which needs to be recycled via a metabolic route termed photorespiration. Photorespiration dissipates energy and most importantly releases previously fixed CO2, thus significantly lowering carbon fixation rate and yield. Engineering plants to omit photorespiratory CO2 release is the goal of the FutureAgriculture consortium and this thesis is part of this collaboration. The consortium aims to establish alternative glycolate-2P recycling routes that do not release CO2. Ultimately, they are expected to increase carbon fixation rates and crop yields. Natural and novel reactions, which require enzyme engineering, were considered in the pathway design process. Here I describe the engineering of two pathways, the arabinose-5P and the erythrulose shunt. They were designed to recycle glycolate-2P via glycolaldehyde into a sugar phosphate and thereby reassimilate glycolate-2P to the Calvin cycle. I used Escherichia coli gene deletion strains to validate and characterize the activity of both synthetic shunts. The strains’ auxotrophies can be alleviated by the activity of the synthetic route, thus providing a direct way to select for pathway activity. I introduced all pathway components to these dedicated selection strains and discovered inhibitions, limitations and metabolic cross talk interfering with pathway activity. After resolving these issues, I was able to show the in vivo activity of all pathway components and combine them into functional modules.. Specifically, I demonstrate the activity of a new-to-nature module of glycolate reduction to glycolaldehyde. Also, I successfully show a new glycolaldehyde assimilation route via arabinose-5P to ribulose-5P. In addition, all necessary enzymes for glycolaldehyde assimilation via L-erythrulose were shown to be active and an L-threitol assimilation route via L-erythrulose was established in E. coli. On their own, these findings demonstrate the power of using an easily engineerable microbe to test novel pathways; combined, they will form the basis for implementing photorespiration bypasses in plants.
Characterisation of gene-regulatory network (GRN) interactions provides a stepping stone to understanding how genes affect cellular phenotypes. Yet, despite advances in profiling technologies, GRN reconstruction from gene expression data remains a pressing problem in systems biology. Here, we devise a supervised learning approach, GRADIS, which utilises support vector machine to reconstruct GRNs based on distance profiles obtained from a graph representation of transcriptomics data. By employing the data fromEscherichia coliandSaccharomyces cerevisiaeas well as synthetic networks from the DREAM4 and five network inference challenges, we demonstrate that our GRADIS approach outperforms the state-of-the-art supervised and unsupervided approaches. This holds when predictions about target genes for individual transcription factors as well as for the entire network are considered. We employ experimentally verified GRNs fromE. coliandS. cerevisiaeto validate the predictions and obtain further insights in the performance of the proposed approach. Our GRADIS approach offers the possibility for usage of other network-based representations of large-scale data, and can be readily extended to help the characterisation of other cellular networks, including protein-protein and protein-metabolite interactions.
Identifying the entirety of gene regulatory interactions in a biological system offers the possibility to determine the key molecular factors that affect important traits on the level of cells, tissues, and whole organisms. Despite the development of experimental approaches and technologies for identification of direct binding of transcription factors (TFs) to promoter regions of downstream target genes, computational approaches that utilize large compendia of transcriptomics data are still the predominant methods used to predict direct downstream targets of TFs, and thus reconstruct genome-wide gene-regulatory networks (GRNs). These approaches can broadly be categorized into unsupervised and supervised, based on whether data about known, experimentally verified gene-regulatory interactions are used in the process of reconstructing the underlying GRN. Here, we first describe the generic steps of supervised approaches for GRN reconstruction, since they have been recently shown to result in improved accuracy of the resulting networks? We also illustrate how they can be used with data from model organisms to obtain more accurate prediction of gene regulatory interactions.
Heterostyly represents a fascinating adaptation to promote outbreeding in plants that evolved multiple times independently. While L-morph individuals form flowers with long styles, short anthers, and small pollen grains, S-morph individuals have flowers with short styles, long anthers, and large pollen grains. The difference between the morphs is controlled by an S-locus "supergene" consisting of several distinct genes that determine different traits of the syndrome and are held together, because recombination between them is suppressed. In Primula, the S locus is a roughly 300-kb hemizygous region containing five predicted genes. However, with one exception, their roles remain unclear, as does the evolutionary buildup of the S locus. Here we demonstrate that the MADS-box GLOBOSA2 (GLO2) gene at the S locus determines anther position. In Primula forbesii S-morph plants, GLO2 promotes growth by cell expansion in the fused tube of petals and stamen filaments beneath the anther insertion point; by contrast, neither pollen size nor male incompatibility is affected by GLO2 activity. The paralogue GLO1, from which GLO2 arose by duplication, has maintained the ancestral B-class function in specifying petal and stamen identity, indicating that GLO2 underwent neofunctionalization, likely at the level of the encoded protein. Genetic mapping and phylogenetic analysis indicate that the duplications giving rise to the style-length-determining gene CYP734A50 and to GLO2 occurred sequentially, with the CYP734A50 duplication likely the first. Together these results provide the most detailed insight into the assembly of a plant supergene yet and have important implications for the evolution of heterostyly.
Starch and Glycogen Analyses
(2020)
For complex carbohydrates, such as glycogen and starch, various analytical methods and techniques exist allowing the detailed characterization of these storage carbohydrates. In this article, we give a brief overview of the most frequently used methods, techniques, and results. Furthermore, we give insights in the isolation, purification, and fragmentation of both starch and glycogen. An overview of the different structural levels of the glucans is given and the corresponding analytical techniques are discussed. Moreover, future perspectives of the analytical needs and the challenges of the currently developing scientific questions are included
Starch and Glycogen Analyses
(2020)
For complex carbohydrates, such as glycogen and starch, various analytical methods and techniques exist allowing the detailed characterization of these storage carbohydrates. In this article, we give a brief overview of the most frequently used methods, techniques, and results. Furthermore, we give insights in the isolation, purification, and fragmentation of both starch and glycogen. An overview of the different structural levels of the glucans is given and the corresponding analytical techniques are discussed. Moreover, future perspectives of the analytical needs and the challenges of the currently developing scientific questions are included
Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.
Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.
Island disharmony refers to the biased representation of higher taxa on islands compared to their mainland source regions and represents a central concept in island biology. Here, we develop a generalizable framework for approximating these source regions and conduct the first global assessment of island disharmony and its underlying drivers. We compiled vascular plant species lists for 178 oceanic islands and 735 mainland regions. Using mainland data only, we modelled species turnover as a function of environmental and geographic distance and predicted the proportion of shared species between each island and mainland region. We then quantified the over- or under-representation of families on individual islands (representational disharmony) by contrasting the observed number of species against a null model of random colonization from the mainland source pool, and analysed the effects of six family-level functional traits on the resulting measure. Furthermore, we aggregated the values of representational disharmony per island to characterize overall taxonomic bias of a given flora (compositional disharmony), and analysed this second measure as a function of four island biogeographical variables. Our results indicate considerable variation in representational disharmony both within and among plant families. Examples of generally over-represented families include Urticaceae, Convolvulaceae and almost all pteridophyte families. Other families such as Asteraceae and Orchidaceae were generally under-represented, with local peaks of over-representation in known radiation hotspots. Abiotic pollination and a lack of dispersal specialization were most strongly associated with an insular over-representation of families, whereas other family-level traits showed minor effects. With respect to compositional disharmony, large, high-elevation islands tended to have the most disharmonic floras. Our results provide important insights into the taxon- and island-specific drivers of disharmony. The proposed framework allows overcoming the limitations of previous approaches and provides a quantitative basis for incorporating functional and phylogenetic approaches into future studies of island disharmony.
Island disharmony refers to the biased representation of higher taxa on islands compared to their mainland source regions and represents a central concept in island biology. Here, we develop a generalizable framework for approximating these source regions and conduct the first global assessment of island disharmony and its underlying drivers. We compiled vascular plant species lists for 178 oceanic islands and 735 mainland regions. Using mainland data only, we modelled species turnover as a function of environmental and geographic distance and predicted the proportion of shared species between each island and mainland region. We then quantified the over- or under-representation of families on individual islands (representational disharmony) by contrasting the observed number of species against a null model of random colonization from the mainland source pool, and analysed the effects of six family-level functional traits on the resulting measure. Furthermore, we aggregated the values of representational disharmony per island to characterize overall taxonomic bias of a given flora (compositional disharmony), and analysed this second measure as a function of four island biogeographical variables. Our results indicate considerable variation in representational disharmony both within and among plant families. Examples of generally over-represented families include Urticaceae, Convolvulaceae and almost all pteridophyte families. Other families such as Asteraceae and Orchidaceae were generally under-represented, with local peaks of over-representation in known radiation hotspots. Abiotic pollination and a lack of dispersal specialization were most strongly associated with an insular over-representation of families, whereas other family-level traits showed minor effects. With respect to compositional disharmony, large, high-elevation islands tended to have the most disharmonic floras. Our results provide important insights into the taxon- and island-specific drivers of disharmony. The proposed framework allows overcoming the limitations of previous approaches and provides a quantitative basis for incorporating functional and phylogenetic approaches into future studies of island disharmony.
Subterranean termites create tunnels (macropores) for foraging that can influence water infiltration and may lead to preferential flow to deeper soil layers. This is particularly important in water limited ecosystems such as semi-arid, agriculturally utilized savannas, which are particularly prone to land degradation and shrub-encroachment. Using termite activity has been suggested as a restoration measure, but their impact on hydrology is neither universal nor yet fully understood. Here, we used highly replicated, small-scale (50 x 50 cm) rain-simulation experiments to analyse the interacting effects of either vegetation (grass dominated vs. shrub dominated sites) or soil texture (sand vs. loamy sand) and termite foraging macropores on infiltration patterns. We used Brilliant Blue FCF as colour tracer to make the flow pathways in paired experiments visible, on either termite-disturbed soil or controls without surface macropores in two semi-arid Namibian savannas (with either heterogeneous soil texture or shrub cover). On highly shrub-encroached plots in the savanna site with heterogeneous soil texture, termite macropores increased maximum infiltration depth and total amount of infiltrated water on loamy sand, but not on sandy soil. In the sandy savanna with heterogeneous shrub cover, neither termite activity nor shrub density affected the infiltration. Termite's effect on infiltration depends on the soil's hydraulic conductivity and occurs mostly under ponded conditions, intercepting run-off. In semi-arid savanna soils with a considerable fraction of fine particles, termites are likely an important factor for soil water dynamics.
A fundamental focus of current ecological and evolutionary research is to illuminate the drivers of animals' success in coping with human-induced rapid environmental change (HIREC). Behavioural adaptations are likely to play a major role in coping with HIREC because behaviour largely determines how individuals interact with their surroundings. A substantial body of research reports behavioural modifications in urban dwellers compared to rural conspecifics. However, it is often unknown whether the observed phenotypic divergence is due to phenotypic plasticity or the product of genetic adaptations. Here, we aimed at investigating (a) whether behavioural differences arise also between rural and urban populations of non-commensal rodents; and (b) whether these differences result from behavioural flexibility or from intrinsic behavioural characteristics, such as genetic or maternal effects. We captured and kept under common environment conditions 42 rural and 52 urban adult common voles (Microtus arvalis) from seven subpopulations along a rural-urban gradient. We investigated individual variation in behavioural responses associated with risk-taking and exploration, in situ at the time of capture in the field and ex situ after 3 months in captivity. Urban dwellers were bolder and more explorative than rural conspecifics at the time of capture in their respective sites (in situ). However, when tested under common environmental conditions ex situ, rural individuals showed little change in their behavioural responses whereas urban individuals altered their behaviour considerably and were consistently shyer and less explorative than when tested in situ. The combination of elevated risk-taking and exploration with high behavioural flexibility might allow urban populations to successfully cope with the challenges of HIREC. Investigating whether the observed differences in behavioural flexibility are adaptive and how they are shaped by additive and interactive effects of genetic make-up and past environmental conditions will help illuminate eco-evolutionary dynamics under HIREC and predict persistence of populations under urban conditions.
Objectives: In this work, a simple and rapid liquid chromatographic method for the simultaneous determination of irbesartan (IRBE) and hydrochlorothiazide (HCT) was developed and validated by reverse phase high performance liquid chromatography (RP-HPLC). <br /> Materials and Methods: Experimental conditions such as different buffer solutions, various pH values, temperature, composition of the mobile phase, and the effect of flow rate were optimized. <br /> Results: The developed RP-HPLC method for these antihypertensive agents was wholly validated and IRBE was detected in the linear range of 0.1-25 mu g mL(-1) and HCT was detected in the linear range of 0.25-25 mu g mL(-1). Moreover, the suggested chromatographic technique was successfully applied for the determination of the drugs in human serum and pharmaceutical dosage forms with limit of detection values of 0.008 mu g mL(-1) for IRBE and 0.012 mu g mL(-1) for HCT. <br /> Conclusion: The proposed rapid analysis method of these antihypertensive drugs can be easily used and applied by pharmaceutical companies for which the analysis time is important.
The P22 tailspike endorhamnosidase confers the high specificity of bacteriophage P22 for some serogroups of Salmonella differing only slightly in their O-antigen polysaccharide. We used several biophysical methods to study the binding and hydrolysis of O-antigen fragments of different lengths by P22 tailspike protein. O-Antigen saccharides of defined length labeled with fluorophors could be purified with higher resolution than previously possible. Small amounts of naturally occurring variations of 0antigen fragments missing the nonreducing terminal galactose could be used to determine the contribution of this part to the free energy of binding to be similar to 7 kJ/mol. We were able to show via several independent lines of evidence that an unproductive binding mode is highly favored in binding over all other possible binding modes leading to hydrolysis. This is true even under circumstances under which the O-antigen fragment is long enough to be cleaved efficiently by the enzyme. The high-affinity unproductive binding mode results in a strong self-competitive inhibition in addition to product inhibition observed for this system. Self-competitive inhibition is observed for all substrates that have a free reducing end rhamnose. Naturally occurring O-antigen, while still attached to the bacterial outer membrane, does not have a free reducing end and therefore does not perform self-competitive inhibition.
Dual glucagon-like peptide-1/glucagon receptor agonists have emerged as promising candidates for the treatment of diabetes and obesity. Issues of degradation sensitivity and rapid renal clearance are addressed, for example, by the conjugation of peptides to fatty acid chains, promoting reversible albumin binding. We use combined dynamic and static light scattering to directly measure the self-assembly of a set of dual peptide agonists based on the exendin-4 structure with varying fatty acid chain lengths in terms of apparent molecular mass and hydrodynamic radius (R-S). We use NMR spectroscopy to gain an insight into the molecular architecture of the assembly. We investigate conformational changes of the monomeric subunits resulting from peptide self-assembly and assembly stability as a function of the fatty acid chain length using circular dichroism and fluorescence spectroscopy. Our results demonstrate that self-assembly of the exendin-4-derived dual agonist peptides is essentially driven by hydrophobic interactions involving the conjugated acyl chains. The fatty acid chain length affects assembly equilibria and the assembly stability, although the peptide subunits in the assembly retain a dynamic secondary structure. The assembly architecture is characterized by juxtaposition of the fatty acyl side chains and a hydrophobic cluster of the peptide moiety. This cluster experiences local conformational changes in the assembly compared to the monomeric unit leading to a reduction in solvent exposure. The N-terminal half of the peptide and a C-terminal loop are not in contact with neighboring peptide subunits in the assemblies. Altogether, our study contributes to a thorough understanding of the association characteristics and the tendency toward self-assembly in response to lipidation. This is important not only to achieve the desired bioavailability but also with respect to the physical stability of peptide solutions.
Dual glucagon-like peptide-1/glucagon receptor agonists have emerged as promising candidates for the treatment of diabetes and obesity. Issues of degradation sensitivity and rapid renal clearance are addressed, for example, by the conjugation of peptides to fatty acid chains, promoting reversible albumin binding. We use combined dynamic and static light scattering to directly measure the self-assembly of a set of dual peptide agonists based on the exendin-4 structure with varying fatty acid chain lengths in terms of apparent molecular mass and hydrodynamic radius (R-S). We use NMR spectroscopy to gain an insight into the molecular architecture of the assembly. We investigate conformational changes of the monomeric subunits resulting from peptide self-assembly and assembly stability as a function of the fatty acid chain length using circular dichroism and fluorescence spectroscopy. Our results demonstrate that self-assembly of the exendin-4-derived dual agonist peptides is essentially driven by hydrophobic interactions involving the conjugated acyl chains. The fatty acid chain length affects assembly equilibria and the assembly stability, although the peptide subunits in the assembly retain a dynamic secondary structure. The assembly architecture is characterized by juxtaposition of the fatty acyl side chains and a hydrophobic cluster of the peptide moiety. This cluster experiences local conformational changes in the assembly compared to the monomeric unit leading to a reduction in solvent exposure. The N-terminal half of the peptide and a C-terminal loop are not in contact with neighboring peptide subunits in the assemblies. Altogether, our study contributes to a thorough understanding of the association characteristics and the tendency toward self-assembly in response to lipidation. This is important not only to achieve the desired bioavailability but also with respect to the physical stability of peptide solutions.