Broad Variation Research Articles

Synthesis of multi-layered perovskite oxyiodides: Impact of number of perovskite layers and type of halide layer for band levels and photocatalytic properties

Layered oxyiodides with a Sillén-Aurivillius structure ([Bi2O2][An−1BnO3n+1][Bi2O2][X]; X = halide, n = number of perovskite layers) have attracted much attention as promising photocatalysts for visible-light-induced water splitting. Changing the number of perovskite layers in oxychlorides provides broad structural variations. However, there are no reports on the synthesis of Sillén-Aurivillius oxyiodides with n ≥ 3 due to unestablished synthetic methods. Three novel oxyiodides, namely, BaBi5Ti3O14I (n = 3), Ba2Bi5Ti4O17I (n = 4), and Ba3Bi5Ti5O20I (n = 5) with triple-, quadruple-, and quintuple-perovskite layers, respectively, were synthesized in this study by investigating and optimizing the synthetic routes in the solid-state reaction. The results reveal that the key to achieving the single-phase synthesis of multi-layered oxyiodides is avoiding the use of low-reactivity Aurivillius compounds as raw materials. The obtained oxyiodides possessed narrower band gaps than their chloride and bromide counterparts, as well as appropriate band levels for water splitting. They functioned as photocatalysts for water (reduction) and oxidation under (UV-) visible light; notably BaBi5Ti3O14I exhibited significantly higher photocatalytic O2 evolution than the other oxyiodides and chloride/bromide counterparts.

Transcrustal and source processes affecting the chemical characteristics of magmas in a hyperactive volcanic zone

Arc magma generation and evolution are affected by transcrustal processes, such as assimilation and fractional crystallisation, and source processes like slab influx into the mantle wedge. However, the relative contribution of these mechanisms remains contentious. The Pleistocene to Holocene Taupo Volcanic Zone (TVZ) is unusually dominated by felsic volcanism with more than 95% of the total eruptive volume corresponding to rhyolitic magmas. Despite the relatively thin crustal basement (∼16–30 km), combined wall rock assimilation and fractional crystallization (AFC) of primary basalt has previously been presented as a necessary means to generate the chemical characteristics of these magmas. This petrogenetic model is here assessed using a new, internally consistent set of major and trace element concentrations, and Sr-Pb isotope data from a suite of basaltic to rhyolitic samples that are representative of the entire TVZ with respect to geographical distribution and age. The dataset was modelled for AFC using the energy- and mass-constrained Magma Chamber Simulator (MCS) and the local Permian to Early Jurassic Torlesse composite terrane basement used as the principal assimilant. Regardless of the intensive parameters employed, the energy- and mass-constrained models presented here fail to realistically reproduce the combined major oxide, trace element, and isotope systematics of the sample set. The Pb isotope ratios of TVZ basalts to rhyolites reveal a broadly linear trend ranging from an unradiogenic (206Pb/204Pb: 18.77) to a more radiogenic crustal endmember (206Pb/204Pb: 18.84). This trend can be reproduced by a composite mélange dominated by the Torlesse terrane (representative of tectonically eroded forearc crust), with some contribution of subducting sediments (GLOSS-II), interacting with the sub-arc mantle to generate the source of the magmas observed in the TVZ. This model is also consistent with Sr-Pb isotope systematics. At New Zealand’s active margin, tectonic erosion has been reported based on geophysical data. Therefore, it is proposed that slab input can have a stronger relevance in the magma generation of the TVZ than previously thought. The broad compositional variations in the TVZ may result from source contamination by a subduction mélange, with differentiation processes within the overriding crust being subordinate.

The impact of small groups on pre- and postcopulatory sexual selection in polyandrous populations.

Sexual selection is a key evolutionary force but varies widely between populations. Two key factors that influence sexual selection are the extent to which females copulate with multiple males (polyandry) and variation in the social environment. Increasing research demonstrates populations are structured by complex socio-sexual networks, and the structure of these networks can influence sexual selection by shaping the relationship between male precopulatory mating success and the intensity of postcopulatory competition. However, comparatively less attention has been dedicated to the influence of group structure on sexual selection and how differences in the size of groups may impact on the relative force of pre- and postcopulatory sexual selection in polyandrous populations. The presence of groups (i.e., group structure) and the size of groups varies widely in nature and forms an implicit part of much experimental sexual selection research under laboratory conditions. Here I use simulations of mating competition within populations that vary in the size of groups they contain, to show that variation in group size, and in particular small groups, can influence sexual selection. Specifically, I show that null expectations for the operation of pre- and postcopulatory sexual selection is governed by the size of groups within populations because smaller group sizes constrain the structure of sexual networks leading to reinforcing episodes of pre- and postcopulatory sexual selection. Given broad variation in group structure in nature and the tendency for experimental sexual selection research to study replicate small groups, these effects have implications for our understanding of the operation of sexual selection in polyandrous populations.

Characterization of Purple Carrot Germplasm for Antioxidant Capacity and Root Concentration of Anthocyanins, Phenolics, and Carotenoids.

The present study characterized a genetically and phenotypically diverse collection of 27 purple and two non-purple (one orange and one yellow) carrot accessions for concentration of root anthocyanins, phenolics, and carotenoids, and antioxidant capacity estimated by four different methods (ORAC, DPPH, ABTS, FRAP), in a partially replicated experimental design comprising data from two growing seasons (2018 and 2019). Broad and significant (p < 0.0001) variation was found among the accessions for all the traits. Acylated anthocyanins (AA) predominated over non-acylated anthocyanins (NAA) in all the accessions and years analyzed, with AA accounting for 55.5-100% of the total anthocyanin content (TAC). Anthocyanins acylated with ferulic acid and coumaric acid were the most abundant carrot anthocyanins. In general, black or solid purple carrots had the greatest TAC and total phenolic content (TPC), and the strongest antioxidant capacities, measured by all methods. Antioxidant capacity, estimated by all methods, was significantly, positively, and moderately-to-strongly correlated with the content of all individual anthocyanins pigments, TAC, and TPC, in both years (r = 0.59-0.90, p < 0.0001), but not with the carotenoid pigments lutein and β-carotene; suggesting that anthocyanins and other phenolics, but not carotenoids, are major contributors of the antioxidant capacity in purple carrots. We identified accessions with high concentration of chemically stable AA, with potential value for the production of food dyes, and accessions with relatively high content of bioavailable NAA that can be selected for increased nutraceutical value (e.g., for fresh consumption).

Contrasting spatial distribution of pioneer versus non‐pioneer saplings in a Taiwanese forest: A multiple scale approach

AbstractDispersal limitation and environmental filtering were recognized as the main dispersal‐based and niche‐based processes responsible for community assembly. These interactions usually leave more spatial signatures in sapling communities and create detectable spatial patterns in different functional types of species. We investigated saplings of pioneer and non‐pioneer species, which facilitated an understanding of species co‐existence and biodiversity recovery. Based upon mapped tree data in the subtropical evergreen broad‐leaved forest dynamics plot in Taiwan, we endeavored to: (1) determine the different spatial scales contributing to distribution patterns of pioneer and non‐pioneer saplings; (2) understand how dispersal limitation affects distribution of pioneer and non‐pioneer saplings; and (3) evaluate the degree to which the different environmental factors explain variation in species composition in pioneer and non‐pioneer saplings. We used the principal coordinates of neighbor matrices (PCNM) method, and variation partitioning to disentangle the contributions of these processes. Fine‐scale spatial patterns were more important for pioneer than for non‐pioneer saplings. Dispersal limitation was the main process influencing the spatial distribution of the non‐pioneer saplings. Environmental filtering was also an important process regulating the spatial distribution of saplings for both functional types, especially for pioneer saplings. Disturbance effects contributed to fine‐scale spatial variation in pioneer saplings, whereas topographic and soil effects contributed to broad and medium scale spatial variation in non‐pioneer saplings. It was evident that different spatial patterns of saplings of different functional types served to facilitate tree regeneration and maintain species co‐existence in this subtropical broad‐leaved forest.

Intraspecific divergence of diploid grass Aegilopscomosa is associated with structural chromosome changes.

Aegilopscomosa Smith in Sibthorp et Smith, 1806 is diploid grass with MM genome constitution occurring mainly in Greece. Two morphologically distinct subspecies - Ae.c.comosa Chennaveeraiah, 1960 and Ae.c.heldreichii (Holzmann ex Boissier) Eig, 1929 are discriminated within Ae.comosa, however, genetic and karyotypic bases of their divergence are not fully understood. We used Fluorescence in situ hybridization (FISH) with repetitive DNA probes and electrophoretic analysis of gliadins to characterize the genome and karyotype of Ae.comosa to assess the level of their genetic diversity and uncover mechanisms leading to radiation of subspecies. We show that two subspecies differ in size and morphology of chromosomes 3M and 6M, which can be due to reciprocal translocation. Subspecies also differ in the amount and distribution of microsatellite and satellite DNA sequences, the number and position of minor NORs, especially on 3M and 6M, and gliadin spectra mainly in the a-zone. Frequent occurrence of hybrids can be caused by open pollination, which, along with genetic heterogeneity of accessions and, probably, the lack of geographic or genetic barrier between the subspecies, may contribute to extremely broad intraspecific variation of GAAn and gliadin patterns in Ae.comosa, which are usually not observed in endemic plant species.

Understanding Patterns of Life History Trait Covariation in an Untapped Resource, the Lab Mouse.

AbstractThrough artificial selection and inbreeding, strains of laboratory mice have been developed that vary in the expression of a single or suite of desired traits valuable to biomedical research. In addition to the selected trait(s), these strains also display variation in pelage color, body size, physiology, and life history. This article exploits the broad phenotypic variation across lab mouse strains to evaluate the relationships between life history and metabolism. Life history variation tends to exist along a fast-slow continuum. There has been considerable interest in understanding the ecological and evolutionary factors underlying life history variation and the physiological and metabolic processes that support them. Yet it remains unclear how these key traits scale across hierarchical levels, as ambiguous empirical support has been garnered at the intraspecific level. Within-species investigations have been thwarted by methodological constraints and environmental factors that obscure the genetic architecture underlying the hypothesized functional integration of life history and metabolic traits. In this analysis, we used the publicly available Mouse Phenome Database by the Jackson Laboratory to investigate the relationships among life history traits (e.g., body size, reproduction, and life span) and metabolic traits (e.g., daily energy expenditure and insulin-like growth factor 1 concentration). Our findings revealed significant variation in reproductive characteristics across strains of mice as well as relationships among life history and metabolic traits. We found evidence of variation along the fast-slow life history continuum, though the direction of some relationships among these traits deviated from interspecific predictions laid out in previous literature. Furthermore, our results suggest that the strength of these relationships are strongest earlier in life.

Challenges and limitations of accelerated stress testing in GDE half-cell set-ups

Commercialisation of proton exchange membrane fuel cells (PEMFCs) depends on accurate and high throughput durability testing at the laboratory scale. With the rotating disk electrode method (RDE) unable to mimic the three-phase boundary scenario in the membrane electrode assembly (MEA), gas diffusion electrode half-cells were proposed for fundamental catalysis research. However, durability testing in such half-cell setups under realistic operational conditions has been limited, and in particular, not yet validated against RDE or FC data. In this paper, an attempt is made to fill part of this knowledge gap by performing accelerated stress tests in thin films, gas diffusion electrodes and membrane electrode assemblies. The results are compared for two selected catalysts with different Pt loading, expected to show broad variations in their degradation behaviour. Accelerated stress tests (ASTs) were performed with various start/stop potentials and load cycles, and the oxygen reduction reaction (ORR) performance studied before and after the AST protocols. The internal resistance of the half-cell was found to be influenced most significantly by gas coverage and temperature changes on the working electrode and must be compensated accordingly. The applied vertex potentials for ASTs after compensation have to be accurate in order to induce the intended degradation phenomena.

Flow Cytometric Investigation of Salinicola halophilus S28 Physiological Response Provides Solid Evidence for Its Uncommon and High Ability to Face Salt-Stress Conditions

In a previous work, some bacterial strains isolated from the Saline di Tarquinia marine salterns (Viterbo, Italy) showed very unusual growth profiles in relation to temperature and salinity variations when grown in solid media. In particular, Salinicola halophilus S28 showed optimal or suboptimal growth in a very wide range of NaCl concentrations, suggesting a great coping ability with salinity variations. These intriguing outcomes did not fit with the general Salinicola halophilus description as a moderately halophilic species. Therefore, this study profiles the actual physiological status of S28 cells subjected to different NaCl concentrations to provide evidence for the actual coping ability of strain S28 with broad salinity variations. Flow cytometry was selected as the evaluation method to study the physiological status of bacterial cells subjected to different salinity levels, monitoring the strain response at different growth phases over 72 h. Strain S28 showed maximal growth at 8% NaCl; however, it grew very well with no statistically significant differences at all salinity conditions (4–24% NaCl). Flow cytometric results provided clear evidence of its actual and strong ability to face increasing salinity, revealing a good physiological response up to 24% of NaCl. In addition, strain S28 showed very similar cell physiological status at all salinity levels, as also indicated by the flat growth profile revealed in the range of 4–24% NaCl. This is the first study regarding the physiological response during the growth of halophilic bacteria under different conditions of salinity via flow cytometry. This technique represents an effective tool for the investigation of the physiological status of each cell, even if it is somehow underrated and underused by microbiologists for this purpose.

Exploration of Compost Soil for the Production of Thermo-Stable Bacillus Protease to Synthesize Bioactive Compounds through Soy Protein Hydrolysis

Application of bioactive peptides (BAPs) is promising due to their potential antimicrobial, antioxidant, agonistic, and ACE inhibition properties. To achieve a stable and active peptide at relatively high pH and temperatures by microbial fermentation, a wide variety of microorganisms need to be explored from diverse habitats, and compost is the excellent source. In an attempt to isolate potent protease-producing bacteria, gelatin-supplemented DM agar medium was used. Out of 140 pure cultures, initial protease production selects isolate D3L/1 (26 U/mL), and 16S rDNA sequencing confirmed it as Bacillus subtilis. Protease production was increased to 55.55 U/mL, with pH 7.5, 1% glucose, 1% casein, 1% ammonium sulfate, for 96 h of fermentation, at 37 °C under 140 rpm of shaking. Ion-exchange, and size-exclusion chromatography, 30 KDa protease was purified up to 4.1-fold (specific activity 3448.62 U/mL; 67.66% yield). The enzyme was active under broad temperatures (60 °C optimum), organic solvents, and pH variations. A total of 5% H2O2 can only reduce 40% of enzyme activity. However, 1 mM, Fe2+, and Cu2+ increased enzyme activity by five times. Soy hydrolysis (SPI) byD3L/1 protease produces bioactive compound (&lt;3 KDa), which confirmed the peptide bond in the far UV region (205 nm, 215 nm, 225 nm, and 280 nm). The compound was ineffective towards Serratia marcescens but active against Escherechia coli (47%), Staphylococcus aureus (28%), and Pseudomonas aeruginosa (12%).

A Genome-Wide Association Study to Identify Novel Candidate Genes Related to Low-Nitrogen Tolerance in Cucumber (Cucumis sativus L.).

Cucumber is one of the most important vegetables, and nitrogen is essential for the growth and fruit production of cucumbers. It is crucial to develop cultivars with nitrogen limitation tolerance or high nitrogen efficiency for green and efficient development in cucumber industry. To reveal the genetic basis of cucumber response to nitrogen starvation, a genome-wide association study (GWAS) was conducted on a collection of a genetically diverse population of cucumber (Cucumis sativus L.) comprising 88 inbred and DH accessions including the North China type, the Eurasian type, the Japanese and South China type mixed subtype, and the South China type subtype. Phenotypic evaluation of six traits under control (14 mM) and treatment (3.5 mM) N conditions depicted the presence of broad natural variation in the studied population. The GWAS results showed that there were significant differences in the population for nitrogen limitation treatment. Nine significant loci were identified corresponding to six LD blocks, three of which overlapped. Sixteen genes were selected by GO annotation associated with nitrogen. Five low-nitrogen stress tolerance genes were finally identified by gene haplotype analysis: CsaV3_3G003630 (CsNRPD1), CsaV3_3G002970 (CsNRT1.1), CsaV3_4G030260 (CsSnRK2.5), CsaV3_4G026940, and CsaV3_3G011820 (CsNPF5.2). Taken together, the experimental data and identification of candidate genes presented in this study offer valuable insights and serve as a useful reference for the genetic enhancement of nitrogen limitation tolerance in cucumbers.

Evaluating individual tree species classification performance across diverse environments

Vegetation species mapping using airborne imaging spectroscopy yields accurate results and is important for advancing conservation objectives and biogeographic studies. As these data become more readily available owing to the upcoming launch of spaceborne imaging spectrometers, it is necessary to understand how these data can be used to consistently classify species across large geographic scales. However, few studies have attempted to map species across multiple ecosystems; therefore, little is known regarding the effect of intra-specific variation on the mapping of a single species across a wide range of environments and among varying backgrounds of other non-target species. To explore this effect, we developed and tested species classification models for Metrosideros polymorpha, a highly polymorphic canopy species endemic to Hawai’i, which is found in a diverse array of ecosystems. We compared the accuracies of support vector machine (SVM) and random forest models trained on canopy reflectance data from each of eight distinct ecosystems (ecosystem-specific) and a universal model trained on data from all ecosystems. When applied to ecosystem-specific test datasets, the ecosystem-specific models outperformed the universal model; however, the universal model retained high (>81%) accuracies across all ecosystems. Additionally, we found that models from ecosystems with broad variation in M. polymorpha canopy traits, as estimated using chemometric equations applied to canopy spectra, accurately predicted M. polymorpha in other ecosystems. While species classifications across ecosystems can yield accurate results, these results will require sampling procedures that capture the intra-specific variation of the target species.

Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing.

The ability to map a proteomic fingerprint to transcriptomic data would master the understanding of how gene expression translates into actual phenotype. In contrast to nucleic acid sequencing, in vitro protein amplification is impossible and no single cell proteomic workflow has been established as gold standard yet. Advances in microfluidic sample preparation, multi-dimensional sample separation, sophisticated data acquisition strategies, and intelligent data analysis algorithms have resulted in major improvements to successfully analyze such tiny sample amounts with steadily boosted performance. However, among the broad variation of published approaches, it is commonly accepted that highest possible sensitivity, robustness, and throughput are still the most urgent needs for the field. While many labs have focused on multiplexing to achieve these goals, label-free SCP is a highly promising strategy as well whenever high dynamic range and unbiased accurate quantification are needed. We here focus on recent advances in label-free single-cell mass spectrometry workflows and try to guide our readers to choose the best method or combinations of methods for their specific applications. We further highlight which techniques are most propitious in the future and which applications but also limitations we foresee for the field.

Care arrangements between family and state – developing hybrid scripts of ageing in a context of migration

Abstract Due to demographic developments, the number of immigrant families with older members is growing across Western Europe. Poised between the different approaches to care in their countries of origin and destination, such families are treading new ground as they negotiate support for older family members. Based on semi-structured interviews with 26 older and younger family members from 20 Turkish immigrant families in Denmark, this article investigates the broad variation in how these families approach caring for older people. At one end of the scale, some families (re)create a traditional Turkish approach to care in which three generations live together and the daughter-in-law is the main care provider. At the other end of the scale, some families follow the Danish approach in which families rely on public care provision. In between these two poles, many families devise a variety of care solutions for their older members that often rely on considerable support by family. Utilising Cati Coe's concept of care-scription, the analysis shows how families negotiate – and sometimes struggle over – who will shoulder which tasks. In the post-migration context, daughters-in-law are often able to retreat from their traditional role of care provider, which in turn increases expectations of daughters' care provisions. In Denmark, which is a relatively gender-equal society, Turkish daughters may seek to make their brothers take on a greater role in the provision of care for their parents, and in some families, the children also turn towards public care provisions to share the burden of parental care. Resistance from older parents may, however, short-circuit this strategy. Overall, the study points both to the difficulties faced by older immigrants with limited host-country language proficiency when utilising public European care provisions and to the complex and unsettled nature of care provisions in immigrant families in Europe today.

Comparing the influence of thinning treatments with low to high residual basal area on red maple transpiration in a temperate mixed forest

Under climate change, forests are expected to experience drier conditions that may increase tree mortality. Silvicultural treatments, such as thinning, have been proposed to reduce moisture competition and to improve forest resistance to drought events. Most studies have investigated the effectiveness of thinning under semi-arid conditions, while little information is available regarding temperate forest responses, together with the residual basal area (BA) that is required to reap the benefits of these treatments. This research aims to understand how the residual BA influences transpiration in mixed temperate forest stands that are dominated by red maple (Acer rubrum) in southeastern Canada. We monitored the sap flux density (Fd) with thermal dissipation-type sensors for 18 red maples spread across three sites that were each thinned to obtain a gradient of residual BA (20, 12.5, 6 m2/ha). The study was conducted during the first growing season following treatment. Low residual BA plots (6 m2/ha) incurred drier atmospheric conditions as shown by a greater vapor pressure deficit (VPD) compared to high residual BA plots (20 m2/ha), although we observed considerable variability between sites. At the tree scale, Fd increased with residual BA, with the most pronounced differences under dry atmospheric conditions: when daily VPD exceeded 1.1 kPa, mean Fd in high residual BA plots was respectively 20 % and 75 % greater than in medium (12.5 m2/ha) and low residual BA plots. At the stand level, we simulated total transpiration considering the stand as only made of red maples. The transpiration in medium and low residual BA plots amounted to 41 % and 79 % of transpiration simulated in the high residual BA plot. Overall, this work highlighted broad variation in response to residual BA treatments, emphasizing the need to better model forest water budgets, and partitioning overstory and understory evapotranspiration to make more adequate residual BA prescriptions in temperate forests.

Age-related differences in cancer relative survival in the United States: A SEER-18 analysis.

Cancer survival has improved since the 1990s, but to different extents across age groups, with a disadvantage for older adults. We aimed to quantify age-related differences in relative survival (RS-1-year and 1-year conditioning on surviving 1 year) for 10 common cancer types by stage at diagnosis. We used data from 18 United States Surveillance Epidemiology and End Results cancer registries and included cancers diagnosed in 2012 to 2016 followed until December 31, 2017. We estimated absolute differences in RS between the 50 to 64 age group and the 75 to 84 age group. The smallest differences were observed for prostate and breast cancers (1.8%-points [95% confidence interval (CI): 1.5-2.1] and 1.9%-points [95% CI: 1.5-2.3], respectively). The largest was for ovarian cancer (27%-points, 95% CI: 24-29). For other cancers, differences ranged between 7 (95% CI: 5-9, esophagus) and 18%-points (95% CI: 17-19, pancreas). Except for pancreatic cancer, cancer type and stage combinations with very high (>95%) or very low (<40%) 1-year RS tended to have smaller age-related differences in survival than those with mid-range prognoses. Age-related differences in 1-year survival conditioning on having survived 1-year were small for most cancer and stage combinations. The broad variation in survival differences by age across cancer types and stages, especially in the first year, age-related differences in survival are likely influenced by amenability to treatment. Future work to measure the extent of age-related differences that are avoidable, and identify how to narrow the survival gap, may have most benefit by prioritizing cancers with relatively large age-related differences in survival (eg, stomach, esophagus, liver and pancreas).

Inorganic phosphate content does not affect oviposition preference in the invasive pest Drosophila suzukii

AbstractThe broad variation in host use among polyphagous insects is well documented but still poorly understood. In numerous pest insects, the proximate mechanisms responsible for variation in oviposition preference among host plants remain to be elucidated. The invasive crop pest, Drosophila suzukii, attacks a wide range of host fruits. Females prefer ovipositing on particular fruit media (blackberry, cherry, blackcurrant) that are rich in phosphorus. As phosphorus is known to be involved in female reproduction in insect species such as Drosophila, it could drive oviposition preference in D. suzukii. Phosphorus is either present as inorganic or organic phosphate in fruits. As the absolute content in macromolecules associated with phosphate in fruits (i.e. proteins and carbohydrates) do not affect oviposition in D. suzukii, we tested for the effect of inorganic phosphate on oviposition preference. We measured the egg‐laying preferences of D. suzukii in a choice environment containing 12 artificial media with increasing content in inorganic phosphate (monopotassium dihydrogen phosphate). In our assay, D. suzukii females did not prefer ovipositing in media with high inorganic phosphate content compared to media with lower inorganic phosphate content. As a confirmation, we verified the previous result of a higher female preference for media made of phosphorus‐rich fruits (blackberry, cherry, blackcurrant). The higher preference for phosphorus‐rich fruits could be driven by macromolecules containing phosphorus (e.g. phospholipids) or by the presence of one or more molecules that do not contain phosphorus, but that happen to be correlated to fruit phosphorus content. Studying the proximate mechanisms driving host use will ultimately help improve the management of D. suzukii and other crop pests.

Genome-wide comparisons reveal broad variations in intraspecific SNP frequencies among species in Agaricomycetes, Basidiomycota

Background:Genome sequence analyses can provide crucial information for understanding population history, speciation, and taxonomy. In Class Agaricomycetes where most mushroom-forming fungi belong, most species so far have been defined based on morphological, ecological, and/or molecular features. At present, there is little information on how species defined based on such features reflect their genome sequence diversity. In this study, we investigated genome-wide single nucleotide polymorphism (SNP) frequencies between strains within species to understand the patterns of variation.Methods:A total of 112 species in 72 genera of Agaricomycetes contained the nuclear and/or mitochondrial genome sequences from at least two strains each in public databases. Together, we obtained 398 and 106 available nuclear and mitochondrial genomes respectively from these taxa. Pairwise strain comparisons of the nuclear and mitochondrial genomes within individual species were conducted to obtain their SNP frequencies.Results:The SNP frequencies between nuclear genomes within individual species ranged 0–7.69% while for the mitochondrial genome, the pairwise strain SNP frequencies ranged 0–4.41%. The Spearman’s non-parametric rank correlation test showed a weak but statistically significant positive correlation between the paired nuclear and mitochondrial genome SNP frequencies. Overall, we observed a significantly higher SNP frequency in the nuclear genome than in the mitochondrial genomes between strains within most species. Interestingly, across the broad Basidiomycetes, the ratios of mitochondrial genome SNPs and nuclear genome SNPs between pairs of strains within each species were almost all lower than 1, with a mean of 0.24.Conclusions:Our analyses revealed broad variations among species in their intraspecific SNP frequencies in both the nuclear and mitochondrial genomes. However, there was broad consensus among the examined species in their mitochondrial to nuclear genome SNP ratios, suggesting that such a ratio could potentially serve as an indicator for genome sequence-based species identification.

A comprehensive characterization of agronomic and end-use quality phenotypes across a quinoa world core collection.

Quinoa (Chenopodium quinoa Willd.), a pseudocereal with high protein quality originating from the Andean region of South America, has broad genetic variation and adaptability to diverse agroecological conditions, contributing to the potential to serve as a global keystone protein crop in a changing climate. However, the germplasm resources currently available to facilitate quinoa expansion worldwide are restricted to a small portion of quinoa's total genetic diversity, in part because of day-length sensitivity and issues related to seed sovereignty. This study aimed to characterize phenotypic relationships and variation within a quinoa world core collection. The 360 accessions were planted in a randomized complete block design with four replicates in each of two greenhouses in Pullman, WA during the summer of 2018. Phenological stages, plant height, and inflorescence characteristics were recorded. Seed yield, composition, thousand seed weight, nutritional composition, shape, size, and color were measured using a high-throughput phenotyping pipeline. Considerable variation existed among the germplasm. Crude protein content ranged from 11.24% to 17.81% (fixed at 14% moisture). We found that protein content was negatively correlated with yield and positively correlated with total amino acid content and days to harvest. Mean essential amino acids values met adult daily requirements but not leucine and lysine infant requirements. Yield was positively correlated with thousand seed weight and seed area, and negatively correlated with ash content and days to harvest. The accessions clustered into four groups, with one-group representing useful accessions for long-day breeding programs. The results of this study establish a practical resource for plant breeders to leverage as they strategically develop germplasm in support of the global expansion of quinoa.

Holistic View on the Structure of Immune Response: Petri Net Model

The simulation of immune response is a challenging task because quantitative data are scarce. Quantitative theoretical models either focus on specific cell-cell interactions or have to make assumptions about parameters. The broad variation of, e.g., the dimensions and abundance between lymph nodes as well as between individual patients hampers conclusive quantitative modeling. No theoretical model has been established representing a consensus on the set of major cellular processes involved in the immune response. In this paper, we apply the Petri net formalism to construct a semi-quantitative mathematical model of the lymph nodes. The model covers the major cellular processes of immune response and fulfills the formal requirements of Petri net models. The intention is to develop a model taking into account the viewpoints of experienced pathologists and computer scientists in the field of systems biology. In order to verify formal requirements, we discuss invariant properties and apply the asynchronous firing rule of a place/transition net. Twenty-five transition invariants cover the model, and each is assigned to a functional mode of the immune response. In simulations, the Petri net model describes the dynamic modes of the immune response, its adaption to antigens, and its loss of memory.