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The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes.
A key in controlling the SARS-CoV-2 pandemic is the assessment of the immune status of the population. We explored the utility of SARS-CoV-2 virus-like particles (VLPs) as antigens to detect specific humoral immune reactions in an enzyme-linked immunosorbent assay (ELISA).
For this purpose, SARS-CoV-2 VLPs were produced from an engineered cell line and characterized by Western blot, ELISA, and nanoparticle tracking analysis.
Subsequently, we collected 42 serum samples from before the pandemic (2014), 89 samples from healthy subjects, and 38 samples from vaccinated subjects. Seventeen samples were collected less than three weeks after infection, and forty-four samples more than three weeks after infection.
All serum samples were characterized for their reactivity with VLPs and the SARS-CoV-2 N- and S-protein.
Finally, we compared the performance of the VLP-based ELISA with a certified in vitro diagnostic device (IVD). In the applied set of samples, we determined a sensitivity of 95.5% and a specificity of 100% for the certified IVD.
There were seven samples with an uncertain outcome. Our VLP-ELISA demonstrated a superior performance, with a sensitivity of 97.5%, a specificity of 100%, and only three uncertain outcomes.
This result warrants further research to develop a certified IVD based on SARS-CoV-2 VLPs as an antigen.
Simple Summary
Urokinase-type plasminogen activator (urokinase, uPA) is a widely discussed biomarker for cancer prognosis and diagnosis. The gold standard for the determination of protein biomarkers in physiological samples is the enzyme-linked immunosorbent assay (ELISA). Here, antibodies are used to detect the specific protein.
In our study, recently published urokinase aptamers were tested for their use in a sandwich assay format as alternative specific recognition elements. Different aptamer combinations were used for the detection of uPA in a sandwich-assay format and a combination of aptamers and antibodies additionally allowed the differentiation of human high and low molecular weight- (HMW- and LMW-) uPA. Hence, uPA aptamers offer a valuable alternative as specific recognition elements for analytical purposes. Since aptamers are easy to synthesize and modify, they can be used as a cost-effective alternative in sandwich assay formats for the detection of uPA in physiological samples.
Abstract
Urokinase-type plasminogen activator (urokinase, uPA) is a frequently discussed biomarker for prognosis, diagnosis, and recurrence of cancer.
In a previous study, we developed ssDNA aptamers that bind to different forms of human urokinase, which are therefore assumed to have different binding regions.
In this study, we demonstrate the development of aptamer-based sandwich assays that use different combinations of these aptamers to detect high molecular weight- (HMW-) uPA in a micro titer plate format.
By combining aptamers and antibodies, it was possible to distinguish between HMW-uPA and low molecular weight- (LMW-) uPA.
For the best performing aptamer combination, we calculated the limit of detection (LOD) and limit of quantification (LOQ) in spiked buffer and urine samples with an LOD up to 50 ng/mL and 138 ng/mL, respectively.
To show the specificity and sequence dependence of the reporter aptamer uPAapt-02-FR, we have identified key nucleotides within the sequence that are important for specific folding and binding to uPA using a fluorescent dye-linked aptamer assay (FLAA). Since uPA is a much-discussed marker for prognosis and diagnosis in various types of cancers, these aptamers and their use in a micro titer plate assay format represent a novel, promising tool for the detection of uPA and for possible diagnostic applications.
Microviridins are a prominent family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) featuring characteristic lactone and lactam rings. Their unusual cage-like architecture renders them highly potent serine protease inhibitors of which individual variants specifically inhibit different types of proteases of pharmacological interest.
While posttranslational modifications are key for the stability and bioactivity of RiPPs, additional attractive properties can be introduced by functional tags.
To date - although highly desirable - no method has been reported to incorporate functional tags in microviridin scaffolds or the overarching class of graspetides.
In this study, a chemoenzymatic in vitro platform is used to introduce functional tags in various microviridin variants yielding biotinylated, dansylated or propargylated congeners.
This straightforward approach paves the way for customized protease inhibitors with built-in functionalities that can help to unravel the still elusive ecological roles and targets of this remarkable class of compounds and to foster applications based on protease inhibition.
Studies investigating the effect of aboveground herbivory on plants often use clipping to simulate the effects of herbivores, for practical reasons. However, herbivore movements and transfer of oral secretions during herbivory may cause a different response in plant physiology and morphology compared to clipping.
While studies have compared effects of real herbivory vs. clipping on biomass production, plant physiology, and shoot morphology, no study has compared such effects on root morphology.
Therefore, we investigated the effect of herbivory by grasshoppers, herbivory simulated by clipping, and no herbivory on root morphological traits of ten grassland plant species. Root morphological traits were differently affected by the two herbivory treatments. Grasshopper herbivory significantly changed root morphology toward thinner roots with increased specific root length and root area, and decreased root tissue density compared to untreated control plants.
Clipping had mostly similar, but weaker effects on root morphology than grasshopper herbivory.
On the species level, grasshopper herbivory led to strongest changes in root morphology in almost all cases. In contrast, depending on the species, clipping resulted in varying root morphological trait values similar to grasshopper-damaged plants, or in some cases, more closely aligned with control plants.
Though clipping was partly able to mimic the effects of herbivory by grasshoppers, results also indicate that, depending on the species, grasshopper herbivory had different but mostly stronger effects. We, therefore, recommend that future studies apply herbivory with real herbivores to better reflect natural responses in plants and related processes that root morphological traits mediate.
The BEEHAVE model simulates the population dynamics and foraging activity of a single honey bee colony (Apis mellifera) in great detail. Although it still makes numerous simplifying assumptions, it appears to capture a wide range of empirical observations.
It could, therefore, in principle, also be used as a tool in beekeeper education, as it allows the implementation and comparison of different management options.
Here, we focus on treatments aimed at controlling the mite Varroa destructor. However, since BEEHAVE was developed in the UK, mite treatment includes the use of a synthetic acaricide, which is not part of Good Beekeeping Practice in Germany.
A practice that consists of drone brood removal from April to June, treatment with formic acid in August/September, and treatment with oxalic acid in November/December. We implemented these measures, focusing on the timing, frequency, and spacing between drone brood removals.
The effect of drone brood removal and acid treatment, individually or in combination, on a mite-infested colony was examined. We quantify the efficacy of Varroa mite control as the reduction of mites in treated bee colonies compared to untreated bee colonies. We found that drone brood removal was very effective, reducing mites by 90% at the end of the first simulation year after the introduction of mites. This value was significantly higher than the 50-67% reduction expected by bee experts and confirmed by empirical studies.
However, literature reports varying percent reductions in mite numbers from 10 to 85% after drone brood removal. The discrepancy between model results, empirical data, and expert estimates indicate that these three sources should be reviewed and refined, as all are based on simplifying assumptions.
These results and the adaptation of BEEHAVE to the Good Beekeeping Practice are a decisive step forward for the future use of BEEHAVE in beekeeper education in Germany and anywhere where organic acids and drone brood removal are utilized.
How predictable is the next move of an animal? Specifically, which factors govern the short- and long-term motion patterns and the overall dynamics of land-bound, plant-eating animals in general and ruminants in particular? To answer this question, we here study the movement dynamics of springbok antelopes Antidorcas marsupialis. We propose several complementary statistical-analysis techniques combined with machine-learning approaches to analyze—across multiple time scales—the springbok motion recorded in long-term GPS tracking of collared springboks at a private wildlife reserve in Namibia. As a result, we are able to predict the springbok movement within the next hour with a certainty of about 20%. The remaining about 80% are stochastic in nature and are induced by unaccounted factors in the modeling algorithm and by individual behavioral features of springboks. We find that directedness of motion contributes approximately 17% to this predicted fraction. We find that the measure for directedeness is strongly dependent on the daily cycle of springbok activity. The previously known daily affinity of springboks to their water points, as predicted from our machine-learning algorithm, overall accounts for only about 3% of this predicted deterministic component of springbok motion. Moreover, the resting points are found to affect the motion of springboks at least as much as the formally studied effects of water points. The generality of these statements for the motion patterns and their underlying behavioral reasons for other ruminants can be examined on the basis of our statistical-analysis tools in the future.
Step selection analysis (SSA) is a common framework for understanding animal movement and resource selection using telemetry data. Such data are, however, inherently autocorrelated in space, a complication that could impact SSA‐based inference if left unaddressed. Accounting for spatial correlation is standard statistical practice when analysing spatial data, and its importance is increasingly recognized in ecological models (e.g. species distribution models). Nonetheless, no framework yet exists to account for such correlation when analysing animal movement using SSA.
Here, we extend the popular method integrated step selection analysis (iSSA) by including a Gaussian field (GF) in the linear predictor to account for spatial correlation. For this, we use the Bayesian framework R‐INLA and the stochastic partial differential equations (SPDE) technique.
We show through a simulation study that our method provides accurate fixed effects estimates, quantifies their uncertainty well and improves the predictions. In addition, we demonstrate the practical utility of our method by applying it to three wolverine (Gulo gulo) tracks.
Our method solves the problems of assuming spatially independent residuals in the SSA framework. In addition, it offers new possibilities for making long‐term predictions of habitat usage.
Protist grazing pressure plays a major role in controlling aquatic bacterial populations, affecting energy flow through the microbial loop and biogeochemical cycles. Predator-escape mechanisms might play a crucial role in energy flow through the microbial loop, but are yet understudied. For example, some bacteria can use planktonic as well as surface-associated habitats, providing a potential escape mechanism to habitat-specific grazers.
We investigated the escape response of the marine bacterium Marinobacter adhaerens in the presence of either planktonic (nanoflagellate: Cafeteria roenbergensis) or surface-associated (amoeba: Vannella anglica) protist predators, following population dynamics over time.
In the presence of V. anglica, M. adhaerens cell density increased in the water, but decreased on solid surfaces, indicating an escape response towards the planktonic habitat. In contrast, the planktonic predator C. roenbergensis induced bacterial escape to the surface habitat. While C. roenbergensis cell numbers dropped substantially after a sharp initial increase, V. anglica exhibited a slow, but constant growth throughout the entire experiment.
In the presence of C. roenbergensis, M. adhaerens rapidly formed cell clumps in the water habitat, which likely prevented consumption of the planktonic M. adhaerens by the flagellate, resulting in a strong decline in the predator population.
Our results indicate an active escape of M. adhaerens via phenotypic plasticity (i.e., behavioral and morphological changes) against predator ingestion.
This study highlights the potentially important role of behavioral escape mechanisms for community composition and energy flow in pelagic environments, especially with globally rising particle loads in aquatic systems through human activities and extreme weather events.
RangeShifter 2.0
(2021)
Process-based models are becoming increasingly used tools for understanding how species are likely to respond to environmental changes and to potential management options. RangeShifter is one such modelling platform, which has been used to address a range of questions including identifying effective reintroduction strategies, understanding patterns of range expansion and assessing population viability of species across complex landscapes. Here we introduce a new version, RangeShifter 2.0, which incorporates important new functionality. It is now possible to simulate dynamics over user-specified, temporally changing landscapes. Additionally, we integrated a new genetic module, notably introducing an explicit genetic modelling architecture, which allows for simulation of neutral and adaptive genetic processes. Furthermore, emigration, transfer and settlement traits can now all evolve, allowing for sophisticated simulation of the evolution of dispersal. We illustrate the potential application of RangeShifter 2.0's new functionality by two examples. The first illustrates the range expansion of a virtual species across a dynamically changing UK landscape. The second demonstrates how the software can be used to explore the concept of evolving connectivity in response to land-use modification, by examining how movement rules come under selection over landscapes of different structure and composition. RangeShifter 2.0 is built using object-oriented C++ providing computationally efficient simulation of complex individual-based, eco-evolutionary models. The code has been redeveloped to enable use across operating systems, including on high performance computing clusters, and the Windows graphical user interface has been enhanced. RangeShifter 2.0 will facilitate the development of in-silico assessments of how species will respond to environmental changes and to potential management options for conserving or controlling them. By making the code available open source, we hope to inspire further collaborations and extensions by the ecological community.
Leishmaniasis is a vector-borne disease caused by protozoal Leishmania parasites. Previous studies have shown that endoperoxides (EP) can selectively kill Leishmania in host cells.
Therefore, we studied in this work a set of new anthracene-derived EP (AcEP) together with their non-endoperoxidic analogs in model systems of Leishmania tarentolae promastigotes (LtP) and J774 macrophages for their antileishmanial activity and selectivity.
The mechanism of effective compounds was explored by studying their reaction with iron (II) in chemical systems and in Leishmania. The correlation of structural parameters with activity demonstrated that in this compound set, active compounds had a LogP(OW) larger than 3.5 and a polar surface area smaller than 100 angstrom(2).
The most effective compounds (IC50 in LtP < 2 mu M) with the highest selectivity (SI > 30) were pyridyl-/tert-butyl-substituted AcEP.
Interestingly, also their analogs demonstrated activity and selectivity. In mechanistic studies, it was shown that EP were activated by iron in chemical systems and in LtP due to their EP group.
However, the molecular structure beyond the EP group significantly contributed to their differential mitochondrial inhibition in Leishmania.
The identified compound pairs are a good starting point for subsequent experiments in pathogenic Leishmania in vitro and in animal models.
Animal societies are structured of dominance hierarchy (DH). DH can be viewed as networks and analyzed by graph theory. We study the impact of state-dependent feedback (winner-loser effect) on the emergence of local dominance structures after pairwise contests between initially equal-ranking members (equal resource-holding-power, RHP) of small and large social groups. We simulated pairwise agonistic contests between individuals with and without a priori higher RHP by Monte-Carlo-method. Random pairwise contests between equal-ranking competitors result in random dominance structures (‘Null variant’) that are low in transitive triads and high in pass along triads; whereas state-dependent feedback (‘Winner-loser variant’) yields centralized ‘star’ structured DH that evolve from competitors with initially equal RHP and correspond to hierarchies that evolve from keystone individuals. Monte-Carlo simulated DH following state-dependent feedback show motif patterns very similar to those of a variety of natural DH, suggesting that state-dependent feedback plays a pivotal role in robust self-organizing phenomena that transcend the specifics of the individual. Self-organization based on state-dependent feedback leads to social structures that correspond to those resulting from pre-existing keystone individuals. As the efficiency of centralized social networks benefits both, the individual and the group, centralization of social networks appears to be an important evolutionary goal.
Small temporary wetlands, like kettle holes, provide many valuable ecosystem functions and serve as refuge habitats in otherwise monotonous agricultural landscapes. However, the mechanisms that maintain biodiversity in these habitats are still poorly understood. In this study, we investigate how three taxa (vascular plants, ground beetles and spiders) respond to small-scale flooding and disturbance gradients in kettle holes as well as kettle hole area. For this purpose, we determined total, hygrophilic and red list species richness for all taxa and activity density for arthropods along transects extending from the edge towards the center of kettle holes. Furthermore, we calculated the community-weighted mean body size for arthropods and seed mass for plants as surrogates for the ability to respond to disturbance. Our analyses revealed that in particular plants and ground beetles showed strong responses along the small-scale spatial gradient. Total plant species richness decreased towards the center, while hygrophilic plant species increased. In contrast, both total and hygrophilic species richness of ground beetles increased towards the center. Spiders showed similar responses as ground beetles, but less pronounced. We found no evidence that disturbance at the edge of kettle holes leads to smaller body sizes or seed masses. However, arthropods in adjacent arable fields (one meter from the kettle hole edge) were particularly small. Kettle hole area had only weak effects on plants, but not on arthropods. Our study indicates that differences in the depth at the drier edge and the moist, regularly flooded center have a large and taxon-dependent influence on the species composition. Therefore, small-scale heterogeneity seems to be an important predictor for the maintenance of species diversity.
Formate dehydrogenases catalyze the reversible oxidation of formate to carbon dioxide. These enzymes play an important role in CO2 reduction and serve as nicotinamide cofactor recycling enzymes. More recently, the CO2-reducing activity of formate dehydrogenases, especially metal-containing formate dehydrogenases, has been further explored for efficient atmospheric CO2 capture. Here, we investigate the nicotinamide binding site of formate dehydrogenase from Rhodobacter capsulatus for its specificity toward NAD+ vs. NADP+ reduction. Starting from the NAD+-specific wild-type RcFDH, key residues were exchanged to enable NADP+ binding on the basis of the NAD+-bound cryo-EM structure (PDB-ID: 6TG9). It has been observed that the lysine at position 157 (Lys157) in the β-subunit of the enzyme is essential for the binding of NAD+. RcFDH variants that had Glu259 exchanged for either a positively charged or uncharged amino acid had additional activity with NADP+. The FdsBL279R and FdsBK276A variants also showed activity with NADP+. Kinetic parameters for all the variants were determined and tested for activity in CO2 reduction. The variants were able to reduce CO2 using NADPH as an electron donor in a coupled assay with phosphite dehydrogenase (PTDH), which regenerates NADPH. This makes the enzyme suitable for applications where it can be coupled with other enzymes that use NADPH.
A minimal light-driven approach was established for studying enzymatic CO2 conversion spectroscopically. The system consists of a photosensitizer Eosin Y, EDTA as a sacrificial electron donor and substrate source, and formate dehydrogenase from Rhodobacter capsulatus (RcFDH) as a biocatalyst. This simplified three-component system provides a photo-triggered control for in situ characterization of the entire catalytic reaction. Direct reduction of RcFDH by the photosensitizer without additional electron carriers was confirmed via UV-Vis spectroscopy, while GC-MS and IR spectroscopy were used to follow photoinduced CO2 generation from EDTA and its subsequent enzymatic reduction, yielding the product formate. Photo-driven and in vitro, dye-based CO2 reduction was inhibited by azide under a mixed (competitive-non-competitive) inhibition mode. IR spectroscopy reveals displacement of the competitively-bound azide by CO2, reflecting an interaction of both with the active site cofactor. This work comprises a proof-of-concept for a new approach to employ light for regulating the reaction of formate dehydrogenases and other CO2 reductases.
Carl Bergmann was an astute naturalist and physiologist. His ideas about animal size and shape were important advances in the pre-Darwinian nineteenth century. Bergmann's rule claims that that in cold climates, large body mass increases the ratio of volume-to-surface area and provides for maximum metabolic heat retention in mammals and birds. Conversely, in warmer temperatures, smaller body mass increases surface area relative to volume and allows for greater heat loss. For humans, we now know that body size and shape are regulated more by social-economic-political-emotional (SEPE) factors as well as nutrition-infection interactions. Temperature has virtually no effect. Bergmann's rule is a "just-so" story and should be relegated to teaching and scholarship about the history of science. That "rule" is no longer acceptable science and has nothing to tell us about physiological anthropology.
Since the first reported case of COVID-19 in 2019 in China and the official declaration from the World Health Organization in March 2021 as a pandemic, fast and accurate diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has played a major role worldwide. For this reason, various methods have been developed, comprising reverse transcriptase-polymerase chain reaction (RT-PCR), immunoassays, clustered regularly interspaced short palindromic repeats (CRISPR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and bio(mimetic)sensors. Among the developed methods, RT-PCR is so far the gold standard. Herein, we give an overview of the MIP-based sensors utilized since the beginning of the pandemic.
Strain NGK35T is a motile, Gram-stain-negative, rod-shaped (1.0-2.1 mu m long and 0.6-0.8 mu m wide), aerobic bacterium that was isolated from plastic-polluted landfill soil. The strain grew at temperatures between 6 and 37 degrees C (optimum, 28 degrees C), in 0-10 % NaCl (optimum, 1 %) and at pH 6.0-9.5 (optimum, pH 7.5-8.5).
It was positive for cytochrome c oxidase, catalase as well as H2S production, and hydrolysed casein and urea. It used a variety of different carbon sources including citrate, lactate and pyruvate.
The predominant membrane fatty acids were C-16:1 cis9 and C-16:0, followed by C-17:0 cyclo and C-18:1 cis11. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine, followed by diphosphatidyglycerol. The only quinone was ubiquinone Q-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK35(T) belongs to the genus Paenalcaligenes (family Alcaligenaceae), appearing most closely related to Paenalcaligenes hominis CCUG 53761A(T) (96.90 %) and Paenalcaligenes suwonensis ABC02-12(T) (96.94 %).
The genomic DNA G+C content of strain NGK35(T) was 52.1 mol%. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Paenalcaligenes.
Based on phenotypic and molecular characterization, strain NGK35(T) can clearly be differentiated from its phylogenetic neighbours establishing a novel species, for which the name Paenalcaligenes niemegkensis sp. nov. is proposed.
The type strain is NGK35T (=DSM 113270(T)=NCCB 100854(T)).
Background:
Polycystic ovary syndrome (PCOS) is an endocrine disease in which related to obesity, metabolic disorders and is considered as one of the main causes of infertility in women. This trial was investigated the effects of green cardamom on the expression of genes implicated in obesity and diabetes among obese women with PCOS.
Methods:
One hundred ninety-four PCOS women were randomly divided two groups: intervention (n = 99; 3 g/day green cardamom) and control groups (n = 95). All of them were given low calorie diet. Anthropometric, glycemic and androgen hormones were assessed before and after 16-week intervention. The reverse transcription-polymerase chain reaction (RT-PCR) method was used to measure fat mass and obesity-associated (FTO), peroxisome proliferative activating receptor- (PPAR-), carnitine palmitoyltransferase 1A (CPT1A), acetyl-CoA carboxylase beta (ACAB), leptin receptor (LEPR), ghrelin, and lamin A/C (LAMIN) genes expression in each group.
Results:
Anthropometric indices were significantly decreased after intervention in both two studied groups. Glycemic indices and androgen hormones were significantly improved in the intervention group compared to the control group. The expression levels of FTO, CPT1A, LEPR, and LAMIN were significantly downregulated compared to control group (P < 0.001), as well as, PPAR-y was significantly upregulated in the intervention group after intervention with green cardamom compared to control group (P < 0.001).
Conclusion:
This current study showed that the administration of green cardamom is a beneficial approach for improving anthropometric, glycemic, and androgen hormones, as well as obesity and diabetes genes expression in PCOS women under the low-calorie diet.
Photosynthetic activity in both algae and cyanobacteria changes in response to cues of predation
(2022)
A plethora of adaptive responses to predation has been described in microscopic aquatic producers.
Although the energetic costs of these responses are expected, with their consequences going far beyond an individual, their underlying molecular and metabolic mechanisms are not fully known.
One, so far hardly considered, is if and how the photosynthetic efficiency of phytoplankton might change in response to the predation cues. Our main aim was to identify such responses in phytoplankton and to detect if they are taxon-specific.
We exposed seven algae and seven cyanobacteria species to the chemical cues of an efficient consumer, Daphnia magna, which was fed either a green alga, Acutodesmus obliquus, or a cyanobacterium, Synechococcus elongatus (kairomone and alarm cues), or was not fed (kairomone alone).
In most algal and cyanobacterial species studied, the quantum yield of photosystem II increased in response to predator fed cyanobacterium, whereas in most of these species the yield did not change in response to predator fed alga.
Also, cyanobacteria tended not to respond to a non-feeding predator. The modal qualitative responses of the electron transport rate were similar to those of the quantum yield.
To our best knowledge, the results presented here are the broadest scan of photosystem II responses in the predation context so far.