Cross-shelf processes of terrigenous organic matter drive mercury speciation on the east siberian shelf in the Arctic Ocean.

The cross-shelf distributions of total mercury (THg), methylmercury (MeHg) and organic and inorganic matter, as well as the presence of the hgcA gene were investigated on the East Siberian Shelf (ESS) to understand the processes underlying the speciation of sedimentary Hg. Samples were collected from 12 stations grouped into four zones based on water depth: inner shelf (5 stations), mid-shelf (3 stations), outer shelf (2 stations), and slope (2 stations). The THg concentration in the surface sediment increased from the inner shelf (0.25 ± 0.023 nmol g-1) toward the slope (0.52 nmol g-1), and, when normalized to total organic carbon content, the THg showed a positive correlation with the clay-to-sand ratio (r2 = 0.48, p = 0.012) and degree of chemical weathering (r2 = 0.79, p = 0.0001). The highest MeHg concentrations (3.0 ± 1.8 pmol g-1), as well as peaks in the S/C ratio (0.012 ± 0.002) of sediment-leached organic matter, were found on the mid-shelf, suggesting that the activities of sulfate reducers control the net Hg(II) methylation rates in the sediment. This was supported by results from a principal component analysis (PCA) performed with Hg species concentrations and sediment-leached organic matter compositions. The site-specific variation in MeHg showed the highest similarity with that of CHONS compounds in the PCA, where Deltaproteobacteria were projected to be putative Hg(II) methylators in the gene analysis. In summary, the hydrodynamic sorting of lithogenic particles appears to govern the cross-shelf distribution of THg, and in situ methylation is considered a major source of MeHg in the ESS sediment.

Corrigendum: Motility increase of Adherent Invasive Escherichia coli (AIEC) induced by a sub-inhibitory concentration of recombinant endolysin LysPA90.

[This corrects the article DOI: 10.3389/fmicb.2022.1093670.].

Digital circuits and neural networks based on acid-base chemistry implemented by robotic fluid handling.

Acid-base reactions are ubiquitous, easy to prepare, and execute without sophisticated equipment. Acids and bases are also inherently complementary and naturally map to a universal representation of "0" and "1." Here, we propose how to leverage acids, bases, and their reactions to encode binary information and perform information processing based upon the majority and negation operations. These operations form a functionally complete set that we use to implement more complex computations such as digital circuits and neural networks. We present the building blocks needed to build complete digital circuits using acids and bases for dual-rail encoding data values as complementary pairs, including a set of primitive logic functions that are widely applicable to molecular computation. We demonstrate how to implement neural network classifiers and some classes of digital circuits with acid-base reactions orchestrated by a robotic fluid handling device. We validate the neural network experimentally on a number of images with different formats, resulting in a perfect match to the in-silico classifier. Additionally, the simulation of our acid-base classifier matches the results of the in-silico classifier with approximately 99% similarity.

Site-specific temporal variation of population dynamics in subalpine endemic plant species.

Endemic plants in high mountains are projected to be at high risk because of climate change. Temporal demographic variation is a major factor affecting population viability because plants often occur in small, isolated populations. Because isolated populations tend to exhibit genetic differentiation, analyzing temporal demographic variation in multiple populations is required for the management of high mountain endemic species. We examined the population dynamics of an endemic plant species, Primula farinosa subsp. modesta, in four subalpine sites over six years. Stage-based transition matrices were constructed, and temporal variation in the projected population growth rate (λ) was analyzed using life table response experiments (LTREs). The variation in λ was primarily explained by the site × year interaction rather than the main effects of the site and year. The testing sites exhibited inconsistent patterns in the LTRE contributions of the vital rates to the temporal deviation of λ. However, within sites, growth or stasis had significant negative correlations with temporal λ deviation. Negative correlations among the contributions of vital rates were also detected within the two testing sites, and the removal of the correlations alleviated temporal fluctuations in λ. The response of vital rates to yearly environmental fluctuations reduced the temporal variation of λ. Such effects manifested especially at two sites where plants exhibited higher plasticity than plants at other sites. Site-specific temporal variation implies that populations of high mountain species likely exhibit asynchronous temporal changes, and multiple sites need to be evaluated for their conservation.

Effects of Seed Endophytic Bacteria on Life History and Reproductive Traits in a Cosmopolitan Weed, Capsella bursa-pastoris.

Diverse bacteria inhabit plant seeds, and at least some of them can enhance plant performance at the early developmental stage. However, it is still inconclusive whether seed bacteria can influence post-germination traits and their contribution to plant fitness. To explore the evolutionary and ecological consequences of seed endophytic bacteria, we isolated four bacterial strains from the seeds of an annual weedy plant species, Capsella bursa-pastoris, and conducted a common garden experiment using seeds inoculated by isolated bacteria. Seeds infected by bacteria tended to germinate in spring rather than in autumn. Bacterial treatment also altered the expression of plant life history and reproductive traits, including flowering dates, rosette diameter at bolting, number of inflorescences, and fruit production. The results of the path analyses suggested that such effects of bacterial treatments were due to bacterial inoculation as well as germination delayed until spring. Spring germinants with bacterial infection showed a weaker association between post-germination traits and relative fitness than those without bacterial infection. These results suggest that seed bacteria likely affect the expression of post-germination traits directly or indirectly by delaying the germination season. An altered contribution of plant traits to relative fitness implies the influence of seed bacteria on the strength of natural selection.

Evaluation of Salmonella Typhimurium Lacking fruR, ssrAB, or hfq as a Prophylactic Vaccine against Salmonella Lethal Infection.

Non-typhoidal Salmonella (NTS) is one of the primary causes of foodborne gastroenteritis; occasionally, it causes invasive infection in humans. Because of its broad host range, covering diverse livestock species, foods of animal origin pose a critical threat of NTS contamination. However, there is currently no licensed vaccine against NTS infection. FruR, also known as Cra (catabolite repressor/activator), was initially identified as the transcriptional repressor of the fructose (fru) operon, and then found to activate or repress the transcription of many different genes associated with carbon and energy metabolism. In view of its role as a global regulator, we constructed a live attenuated vaccine candidate, ΔfruR, and evaluated its prophylactic effect against NTS infection in mice. A Salmonella Typhimurium mutant strain lacking fruR was defective in survival inside macrophages and exhibited attenuated virulence in infected mice. Immunization with the ΔfruR mutant stimulated the production of antibodies, including the IgG, IgM, and IgG subclasses, and afforded a protection of 100% to mice against the challenge of lethal infection with a virulent Salmonella strain. The prophylactic effect obtained after ΔfruR immunization was also validated by the absence of signs of hepatosplenomegaly, as these mice had comparable liver and spleen weights in comparison with healthy mice. These results suggest that the ΔfruR mutant strain can be further exploited as a promising vaccine candidate against Salmonella lethal infection.

Genotype-Specific Plastic Responses to Seed Bacteria under Drought Stress in Lactuca serriola.

Recent studies have demonstrated that seed-borne bacteria can enhance the performance of invasive plants in novel introduced habitats with environmental stresses. The effect of this plant-bacteria interaction may vary with plant species or even genotype; however, the genotype-dependent effects of seed bacteria have rarely been assessed. In this study, we examined the effects of bacterial strains isolated from seeds on the genotypes of an invasive xerophytic plant, Lactuca serriola. Plant genotypes were grown under drought conditions, and their plastic responses to bacterial infections were evaluated. Some genotypes produced more biomass, whereas others produced less biomass in response to infection with the same bacterial strain. Notably, the quantity of root-adhering soil depended on the bacterial treatment and plant genotypes and was positively correlated with the plastic responses of plant performance. Because tested bacteria could colonize the plant rhizosphere, bacterial infection appears to induce the differential formation of soil rhizosheaths among plant genotypes, consequently affecting the maintenance of soil water content under drought conditions. Given that drought tolerance is a critical attribute for the invasive success of L. serriola, these results imply that bacterial symbionts can facilitate the establishment of alien plant species, but their effects are likely genotype-specific.

CsRCI2D enhances high-temperature stress tolerance in Camelina sativa L. through endo-membrane trafficking from the plasma membrane.

Rare Cold Inducible 2s (RCI2s) are hydrophobic proteins in cell membranes that participate in abiotic stress tolerance mechanisms. Additionally, they are used as traceable membrane trafficking markers in endocytosis studies. Plants regulate cell homeostasis through endocytosis by limiting the activity of plasma membrane transporter proteins to adapt to stressful conditions. In this study, we found high temperature (HT) stress-induced membrane trafficking of RCI2D in Camelina sativa L. The gene expression and protein synthesis were increased by HT stress at 37 °C. Moreover, rapid membrane trafficking of CsRCI2D was traced by multiple-phase membrane fractionation using sucrose density gradients and compared with CsRCI2E/F/G from the same protein family subgroup. The distribution of CsRCI2s was shown to be similar to that of the clathrin heavy chain, which is known as a major endocytosis protein. Subcellular localization of CsRCI2D was observed in the plasma membrane and endo-membranes and overlapped with membrane lipids. CsRCI2D co-localized with lipids, and its overexpression increased the intracellular lipid content compared to that of wild-type camelina. Moreover, transgenic camelina lines showed enhanced HT stress tolerance during germination and hypocotyl elongation when compared to the wild type. These results suggest that HT-induced CsRCI2D membrane trafficking enhances HT stress tolerance in camelina.

Variation of the seed endophytic bacteria among plant populations and their plant growth-promoting activities in a wild mustard plant species, Capsella bursa-pastoris.

Recent studies have revealed that some bacteria can inhabit plant seeds, and they are likely founders of the bacterial community in the rhizosphere of or inside plants at the early developmental stage. Given that the seedling establishment is a critical fitness component of weedy plant species, the effects of seed endophytic bacteria (SEB) on the seedling performance are of particular interest in weed ecology. Here, we characterized the SEB in natural populations of Capsella bursa-pastoris, a model species of weed ecology. The composition of endophytic bacterial community was evaluated using deep sequencing of a 16S rDNA gene fragment. Additionally, we isolated bacterial strains from seeds and examined their plant growth-promoting traits. Actinobacteria, Firmicutes, Alpha-, and Gammaproteobacteria were major bacterial phyla inside seeds. C. bursa-pastoris natural populations exhibited variable seed microbiome such that the proportion of Actinobacteria and Alphaproteobacteria differed among populations, and 60 out of 82 OTUs occurred only in a single population. Thirteen cultivable bacterial species in six genera (Bacillus, Rhodococcus, Streptomyces, Staphylococcus, Paenibacillus, Pseudomonas) were isolated, and none of them except Staphylococcus haemolyticus were previously reported as seed endophytes. Eight isolates exhibited plant growth-promoting traits like phosphate solubilization activity, indole-3-acetic acid, or siderophore production. Despite the differences in the bacterial communities among plant populations, at least one isolated strain from each population stimulated shoot growth of either C. bursa-pastoris or its close relative A. thaliana when grown with plants in the same media. These results suggest that a weedy plant species, C. bursa-pastoris, contains bacterial endophytes inside their seeds, stimulating seedling growth and thereby potentially affecting seedling establishment.

Relationship between oxidative stress and lifespan in Daphnia pulex.

Macromolecular damage leading to cell, tissue and ultimately organ dysfunction is a major contributor to aging. Intracellular reactive oxygen species (ROS) resulting from normal metabolism cause most damage to macromolecules and the mitochondria play a central role in this process as they are the principle source of ROS. The relationship between naturally occurring variations in the mitochondrial (MT) genomes leading to correspondingly less or more ROS and macromolecular damage that changes the rate of aging associated organismal decline remains relatively unexplored. MT complex I, a component of the electron transport chain (ETC), is a key source of ROS and the NADH dehydrogenase subunit 5 (ND5) is a highly conserved core protein of the subunits that constitute the backbone of complex I. Using Daphnia as a model organism, we explored if the naturally occurring sequence variations in ND5 correlate with a short or long lifespan. Our results indicate that the short-lived clones have ND5 variants that correlate with reduced complex I activity, increased oxidative damage, and heightened expression of ROS scavenger enzymes. Daphnia offers a unique opportunity to investigate the association between inherited variations in components of complex I and ROS generation which affects the rate of aging and lifespan.

Salmonella Typhimurium lacking phoBR as a live vaccine candidate against poultry infection.

Salmonella enterica serovar Typhimurium, with a broad-host range, is a predominant cause of non-typhoidal Salmonella infection in humans, and the infectious source is highly associated with food animals, especially poultry. Considering the horizontal transmission of S. Typhimurium from farm animals to humans, vaccination has been strongly recommended in industrial animals. In an effort to eradicate S. Typhimurium in poultry farms, a live candidate vaccine strain lacking the phoBR genes, which encode the PhoB/PhoR two-component regulatory system responsible for cellular phosphate signaling, was evaluated in mice and chickens. Lack of the phoBR genes promoted overgrowth of intracellular Salmonella. However, notably, in BALB/c mouse models, the ΔphoBR mutant showed attenuated virulence and instead, provided protection against infection with virulent Salmonella, thereby clearing out Salmonella in the spleen and liver. Accordingly, immunization with the ΔphoBR mutant increased immunoglobulin (Ig)G and IgM antibody responses and also tended to increase the IgG2a/IgG1 ratio, which is indicative of T helper (Th)1-mediated cellular immunity. In chicken challenge models, immunization with the ΔphoBR mutant significantly boosted the production of IgG and IgM antibodies after the second vaccination. The vaccinated chickens ceased fecal shedding of challenged Salmonella earlier than the non-vaccinated ones and showed no Salmonella in their caecum and ileum. These results demonstrate the potential of the S. Typhimurium ΔphoBR mutant as a vaccine in chickens.

Dioxygen reactivity of a biomimetic [4Fe-4S] compound exhibits [4Fe-4S] to [2Fe-2S] cluster conversion.

Fumarate and nitrate reductase (FNR) is a gene regulatory protein that controls anaerobic to aerobic respiration in Escherichia coli, for which O2 serves as a control switch to induce a protein structural change by converting [4Fe-4S] cofactors to [2Fe-2S] clusters. Although biomimetic models can aid in understanding the complex functions of their protein counterparts, the inherent sensitivity of discrete [Fe-S] molecules to aerobic conditions poses a unique challenge to mimic the O2-sensing capability of FNR. Herein, we report unprecedented biomimetic O2 reactivity of a discrete [4Fe-4S] complex, [Fe4S4(SPhF)4]2- (1) where SPhF is 4-fluorothiophenolate, in which the reaction of 1 with O2(g) in the presence of thiolate produces its [2Fe-2S] analogue, [Fe2S2(SPhF)4]2- (2), at room temperature. The cluster conversion of 1 to 2 can also be achieved by employing disulfide as an oxidant under the same reaction conditions. The [4Fe-4S] to [2Fe-2S] cluster conversion by O2 was found to be significantly faster than that by disulfide, while the reaction with disulfide produced higher yields of 2.

Retroreflection-based sandwich type affinity sensing of isothermal gene amplification products for foodborne pathogen detection.

Loop-mediated isothermal amplification (LAMP) is an outstanding method for molecular diagnostics, as the rapid, specific, and sensitive amplification of target genes is possible. However, it is necessary to measure fluorescence in the quantitative analysis of LAMP products, so a sophisticated optical setup is required. This study tried to develop a novel sensing method that can quantify target analytes with simple equipment, such as nonspectroscopic white light and a CMOS camera. To achieve this, a retroreflective Janus particle (RJP) as a probe and specially designed loop primers, fluorescein isothiocyanate (FITC)- and biotin-modified loop primers, were introduced into the LAMP system. By performing LAMP in the presence of designed primers, double-stranded amplicons possessing FITC and biotin labels at each end are generated in proportion to the quantity of the target pathogen. Using the anti-FITC antibody-modified sensing surface and streptavidin-conjugated RJP probes, the amplicons can be captured in sandwich-configuration and detected under nonspectroscopic conditions composed of white light and a camera. To confirm the feasibility of the sensing system, the invA gene of Salmonella was selected as the target. It was possible to quantitatively analyze the Salmonella concentration from 0 to 106 colony-forming units, sufficiently covering the required detection range. In addition, quantitative analyses of pathogens in contaminated food sources, including milk and chicken meat, were successfully conducted with a limit of detection of 10 CFU.

Motility increase of adherent invasive Escherichia coli (AIEC) induced by a sub-inhibitory concentration of recombinant endolysin LysPA90.

Endolysins are bacteriophage enzymes required for the eruption of phages from inside host bacteria via the degradation of the peptidoglycan cell wall. Recombinant endolysins are increasingly being seen as potential antibacterial candidates, with a number currently undergoing clinical trials. Bacteriophage PBPA90 infecting Pseudomonas aeruginosa harbors a gene encoding an endolysin, lysPA90. Herein, recombinant LysPA90 demonstrated an intrinsic antibacterial activity against Escherichia coli in vitro. It was observed that a sub-inhibitory concentration of the recombinant protein induced the upregulation of genes related to flagella biosynthesis in a commensal E. coli strain. Increases in the number of bacterial flagella, and in motility, were experimentally substantiated. The treatment caused membrane stress, leading to the upregulation of genes rpoE, rpoH, dnaK, dnaJ, and flhC, which are upstream regulators of flagella biosynthesis. When adherent invasive Escherichia coli (AIEC) strains were treated with subinhibitory concentrations of the endolysin, bacterial adhesion and invasion into intestinal epithelial Caco-2 cells was seen to visibly increase under microscopic examination. Bacterial counting further corroborated this adhesion and invasion of AIEC strains into Caco-2 cells, with a resultant slight decrease in the viability of Caco-2 cells then being observed. Additionally, genes related to flagella expression were also upregulated in the AIEC strains. Finally, the enhanced expression of the proinflammatory cytokine genes TNF-α, IL-6, IL-8, and MCP1 in Caco-2 cells was noted after the increased invasion of the AIEC strains. While novel treatments involving endolysins offer great promise, these results highlight the need for the further exploration of possible unanticipated and unintended effects.

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity.

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

Controlled Protonation of [2Fe-2S] Leading to MitoNEET Analogues and Concurrent Cluster Modification.

MitoNEET, a key regulatory protein in mitochondrial energy metabolism, exhibits a uniquely ligated [2Fe-2S] cluster with one histidine and three cysteines. This unique cluster has been postulated to sense the redox environment and release Fe-S cofactors under acidic pH. Reported herein is a synthetic system that shows how [2Fe-2S] clusters react with protons and rearrange their coordination geometry. The low-temperature stable, site-differentiated clusters [Fe2S2(SPh)3(CF3COO)]2- and [Fe2S2(SPh)3(py)]- have been prepared via controlled protonation below -35 °C and characterized by NMR, UV-vis, and X-ray absorption spectroscopy. Both complexes exhibit anodically shifted redox potentials compared to [Fe2S2(SPh)4]2- and convert to [Fe4S4(SPh)4]2- upon warming to room temperature. The current study provides insight into how mitoNEET releases its [2Fe-2S] in response to highly tuned acidic conditions, the chemistry of which may have further implications in Fe-S biogenesis.

Differential plastic responses to temperature and nitrogen deposition in the subalpine plant species, Primula farinosa subsp. modesta.

Future environmental changes are projected to threaten plant populations near mountaintops, but plastic responses of plant traits that are related to demographic parameters may reduce the detrimental effects of altered environments. Despite its ecological significance, little is known about the intraspecific variation of plasticity in alpine plant species such as Primula farinosa subsp. modesta. In this study, we investigated the plastic responses of plants at the early developmental stage from four P. farinosa natural populations in response to temperature and nitrogen deposition under laboratory conditions. Measured traits included plant survival, leaf number, rosette diameter, carbon assimilation rate and leaf chlorophyll content. In addition, we conducted a demographic survey of the natural populations to assess the plant's performance at the early developmental stage in the field and evaluate the ecological implications of our experimental treatments. The seedling stage contributed to the projected population growth rate in natural conditions, and the growth and survival of seedlings in the field were comparable to those grown in the control treatment. In response to high temperature, plants exhibited lower survival but produced larger rosettes with more leaves. Nitrogen deposition had little effect on plant survival and plant size; however, it increased plant survival in one population and altered the effect of temperature on the carbon assimilation rate. Populations exhibited differential plasticity indexes of measured traits in response to environmental treatments. These results suggest that even though the plants suffer from high early mortality under increasing temperature, stimulated growth at a high temperature potentially contributes to the persistence of P. farinosa natural populations. Natural populations might face differential extinction risks due to distinctive plastic responses to altered environments.