s-CorrPlot: An Interactive Scatterplot for Exploring Correlation

The evolution of the duckweed ionome mirrors losses in structural complexity

BACKGROUND AND AIMS

The duckweeds (Lemnaceae) consist of 36 species exhibiting impressive phenotypic variation, including the progressive evolutionary loss of a fundamental plant organ, the root. Loss of roots and reduction of vascular tissues in recently derived taxa occur in concert with genome expansions of ≤14-fold. Given the paired loss of roots and reduction in structural complexity in derived taxa, we focus on the evolution of the ionome (whole-plant elemental contents) in the context of these fundamental changes in body plan. We expect that progressive vestigiality and eventual loss of roots might have both adaptive and maladaptive consequences that are hitherto unknown.

METHODS

We quantified the ionomes of 34 accessions in 21 species across all duckweed genera, spanning 70 Myr in this rapidly cycling plant (doubling times are as rapid as ~24 h). We related both micro- and macroevolutionary ionome contrasts to body plan remodelling and showed nimble microevolutionary shifts in elemental accumulation and exclusion in novel accessions.

KEY RESULTS

We observed a robust directional trend in calcium and magnesium levels, decreasing from the ancestral representative Spirodela genus towards the derived rootless Wolffia, with the latter also accumulating cadmium. We also identified abundant within-species variation and hyperaccumulators of specific elements, with this extensive variation at the fine (as opposed to broad) scale.

CONCLUSIONS

These data underscore the impact of root loss and reveal the very fine scale of microevolutionary variation in hyperaccumulation and exclusion of a wide range of elements. Broadly, they might point to trade-offs not well recognized in ionomes.

Unveiling the evolution of phytoplankton communities: Decades-long insights into the southern Yellow Sea, China (1959-2023)

We obtained historical and observational data on phytoplankton communities from 1959 to 2023 to explore the responses of the phytoplankton community structure to long-term environmental changes in the southern Yellow Sea (SYS), China. The results revealed a decrease in the proportions of diatom cell abundance within the phytoplankton community by 8 %, accompanied by a corresponding increase in that of dinoflagellates. Dominant phytoplankton species were mainly chain-forming diatoms before 2000, and large dinoflagellate species from the genera Tripos and Noctiluca increased their dominance after 2000. Warm-water phytoplankton species have increased in dominance over the study period. Correlation analysis revealed that the ocean warming and alterations in nutrient structure (N/P and Si/N ratios) were mostly responsible for the long-term evolution trend, and these changes may result in an increase in dinoflagellate harmful algal blooms, reduced efficiency of the biological carbon pump, and heightened hypoxia in the future, which should draw our attention.

Physiological adaptation to irradiance in duckweeds is species and accession specific and depends on light habitat niche

Duckweeds span 36 species of free-floating aquatic organisms with body sizes ranging from 2 mm to 10 mm, where each plant body plan is reduced to a largely leaf-like structure. As an emerging crop, their fast growth rates offer potential for cultivation in closed systems. We describe a novel UK collection derived from low light (dLL) or high light (dHL) habitats, profiled for growth, photosynthesis, and photoprotection (non-photochemical quenching, NPQ) responses. Twenty-three accessions of three Lemna species and one Spirodela polyrhiza were grown under relatively low light (LL: 100 μmol m-2 s-1) and high light (HL: 350 μmol m-2 s-1) intensities. We observed broad within- and between-species level variation in photosynthesis acclimation. Duckweeds grown under HL exhibited a lower growth rate, biomass, chlorophyll, and quantum yield of photosynthesis. In HL compared with LL, carotenoid de-epoxidation state and NPQ were higher, whilst PSII efficiency (φPSII) and Chl a:b ratios were unchanged. The dLL plants showed relatively stronger acclimation to HL compared with dHL plants, especially Lemna japonica accessions. These achieved faster growth in HL with concurrent higher carotenoid levels and NPQ, and less degradation of chlorophyll. We conclude that these data support local adaptation to the light environment in duckweed affecting acclimation in controlled conditions.

Longitudinal Distribution Map of the Active Components and Endophytic Fungi in Angelica sinensis (Oliv.) Diels Root and Their Potential Correlations

The three distinct medicinal parts of Angelica sinensis (Oliv.) Diels (Ang) roots are the head, body, and tail (ARH, ARB, and ART, respectively). How endophytic fungi shape the differences in metabolic components among these parts remains unclear. We quantified the distribution of active components and endophytic fungi along the ARH, ARB, and ART and their relationships. Based on the metabolic components and their abundances detected via non-target metabolism, the different medicinal parts were distinguishable. The largest number of dominant metabolic components was present in ART. The difference between ART and ARH was the greatest, and ARB was in a transitional state. The dominant active molecules in ART highlight their effects in haemodynamics improvement, antibacterial, anti-inflammatory, and hormone regulation, while ARH and ARB indicated more haemostasis, blood enrichment, neuromodulation, neuroprotection and tranquilisation, hepatoprotection, and antitumour activities than that of ART. The ARHs, ARBs, and ARTs can also be distinguished from each other based on the endophytic fungi at the microbiome level. The most dominant endophytic fungi were distributed in ART; the differences between ART and ARH were the largest, and ARB was in a transition state, which is consistent with the metabolite distributions. Structural equation modelling showed that the endophytic fungi were highly indicative of the metabolic components. Correlation analysis further identified the endophytic fungi significantly positively correlated with important active components, including Condenascus tortuosus, Sodiomyces alcalophilus, and Pleotrichocladium opacum. The bidirectional multivariate interactions between endophytic fungi and the metabolic components shape their spatial variations along the longitudinal direction in the Ang root.

Comparative transcriptome analysis revealed that auxin and cell wall biosynthesis play important roles in the formation of hollow hearts in cucumber

BACKGROUND

Hollow heart is a kind of physiological defect that seriously affects the yield, quality, and economic value of cucumber. However, the formation of hollow hearts may relate to multiple factors in cucumber, and it is necessary to conduct analysis.

RESULTS

In this study, hollow and non-hollow fruits of cucumber K07 were used for comparative transcriptome sequencing and analysis. 253 differentially expressed genes and 139 transcription factors were identified as being associated with the formation of hollow hearts. Hormone (auxin) signaling and cell wall biosynthesis were mainly enriched in GO and KEGG pathways. Expression levels of key genes involved in indole-3-acetic acid biosynthesis in carpel were lower in the hollow fruits than non-hollow fruits, while there was no difference in the flesh. The concentration of indole-3-acetic also showed lower in the carpel than flesh. The biosynthetic pathway and content analysis of the main components of the cell wall found that lignin biosynthesis had obvious regularity with hollow heart, followed by hemicellulose and cellulose. Correlation analysis showed that there may be an interaction between auxin and cell wall biosynthesis, and they collectively participate in the formation of hollow hearts in cucumber. Among the differentially expressed transcription factors, MYB members were the most abundant, followed by NAC, ERF, and bHLH.

CONCLUSIONS

The results and analyses showed that the low content of auxin in the carpel affected the activity of enzymes related to cell wall biosynthesis at the early stage of fruit development, resulting in incomplete development of carpel cells, thus forming a hollow heart in cucumber. Some transcription factors may play regulatory roles in this progress. The results may enrich the theory of the formation of hollow hearts and provide a basis for future research.

Chia seeds oil ameliorate chronic immobilization stress-induced neurodisturbance in rat brains via activation of the antioxidant/anti-inflammatory/antiapoptotic signaling pathways

Chronic immobilization stress plays a key role in several neuropsychiatric disorders. This investigation assessed the possible ameliorative effect of chia seed oil (CSO) against the neurodisturbance-induced in rats by chronic immobilization. Rats were randomly allocated into control, CSO (1 ml/kg b.wt./orally), restrained (6 h/day), CSO pre-restraint, and CSO post-restraint for 60 days. Results revealed a significant reduction in serum corticosterone level, gene expression of corticotrophin-releasing factor, pro-inflammatory cytokines, and oxidative biomarkers in restrained rats treated with CSO. The histopathological findings revealed restoring necrosis and neuronal loss in CSO-treated-restraint rats. The immunohistochemical evaluation revealed a significant reduction in the immuno-expression of caspase-3, nuclear factor kappa B, interleukin-6, and cyclooxygenase-2 (COX-2), and an elevation of calbindin-28k and synaptophysin expression compared to non-treated restraint rats. The molecular docking showed the CSO high affinity for several target proteins, including caspase-3, COX-2, corticotropin-releasing hormone binding protein, corticotropin-releasing factor receptors 1 and 2, interleukin-1 receptor types 1 and 2, interleukin-6 receptor subunits alpha and beta. In conclusion, CSO emerges as a promising candidate against stress-induced brain disruptions by suppressing inflammatory/oxidative/apoptotic signaling pathways due to its numerous antioxidant and anti-inflammatory components, mainly α-linolenic acid. Future studies are necessary to evaluate the CSO therapeutic impacts in human neurodisturbances.

Mass spectrometry-based metabolite profiling reveals functional seasonal shifts in the metabolome of Zygophyllum dumosum Boiss and its relation to environmental conditions

MAIN CONCLUSION

A multi-year study of perennial Z. dumosum shows a consistent seasonal pattern in the changes of petiole metabolism, involving mainly organic acids, polyols, phenylpropanoids, sulfate conjugates, and piperazines. GC-MS and UPLC-QTOF-MS-based metabolite profiling was performed on the petioles of the perennial desert shrub Zygophyllum dumosum Boiss (Zygophyllaceae). The petioles, which are physiologically functional throughout the year and, thus, exposed to seasonal rhythms, were collected every month for 3 years from their natural ecosystem on a southeast-facing slope. Results showed a clear multi-year pattern following seasonal successions, despite different climate conditions, i.e., rainy and drought years, throughout the research period. The metabolic pattern of change encompassed an increase in the central metabolites, including most polyols, e.g., stress-related D-pinitol, organic and sugar acids, and in the dominant specialized metabolites, which were tentatively identified as sulfate, flavonoid, and piperazine conjugates during the summer-autumn period, while significantly high levels of free amino acids were detected during the winter-spring period. In parallel, the levels of most sugars (including glucose and fructose) increased in the petioles at the flowering stage at the beginning of the spring, while most of the di- and tri-saccharides accumulated at the beginning of seed development (May-June). Analysis of the conserved seasonal metabolite pattern of change shows that metabolic events are mostly related to the stage of plant development and its interaction with the environment and less to environmental conditions per se.

Physicochemical Parameters, Antioxidant Capacity, and Antimicrobial Activity of Honeys from Tropical Forests of Colombia: Apis mellifera and Melipona eburnea

Honey is a functional food used worldwide and recognized for its multiple health benefits. In the present study, the physicochemical and antioxidant properties of honey produced by two species of bees (Melipona eburnea and Apis mellifera) in two seasons were evaluated. In addition, the antimicrobial activity of honey against three bacterial strains was studied. The quality of honey analyzed by LDA (linear discriminant analysis) showed four clusters mediated by the interaction, the bee species, and the collection season resulting from a multivariate function of discrimination. The physicochemical properties of the honey produced by A. mellifera met the requirements of the Codex Alimentarius, while the M. eburnea honey had moisture values outside the established ranges of the Codex. Antioxidant activity was higher in the honey of A. mellifera, and both kinds of honey showed inhibitory activity against S. typhimurium ATCC 14028 and L. monocytogenes ATCC 9118. E. coli ATCC 25922 showed resistance to the analyzed honey.

Ecological linkages between biotechnologically relevant autochthonous microorganisms and phenolic compounds in sugar apple fruit (Annona squamosa L.)

Our study investigated the potential of Annona squamosa (L.) fruit as a reservoir of yeasts and lactic acid bacteria having biotechnological implications, and phenolics capable of modifying the ecology of microbial consortia. Only a single species of lactic acid bacteria (Enterococcus faecalis) was identified, while Annona fruit seemed to be a preferred niche for yeasts (Saccharomyces cerevisiae, Hanseniaspora uvarum), which were differentially distributed in the fruit. In order to identify ecological implications for inherent phenolics, the antimicrobial potential of water- and methanol/water-soluble extracts from peel and pulp was studied. Pulp extracts did not show any antimicrobial activity against the microbial indicators, while some Gram-positive bacteria (Staphylococcus aureus, Staphylococcus saprophyticus, Listeria monocytogenes, Bacillus megaterium) were susceptible to peel extracts. Among lactic acid bacteria used as indicators, only Lactococcus lactis and Weissella cibaria were inhibited. The chemical profiling of methanol/water-soluble phenolics from Annona peel reported a full panel of 41 phenolics, mainly procyanidins and catechin derivatives. The antimicrobial activity was associated to specific compounds (procyanidin dimer type B [isomer 1], rutin [isomer 2], catechin diglucopyranoside), in addition to unidentified catechin derivatives. E. faecalis, which was detected in the epiphytic microbiota, was well adapted to the phenolics from the peel. Peel phenolics had a growth-promoting effect toward the autochthonous yeasts S. cerevisiae and H. uvarum.

Probiotics (Lactobacillus plantarum HNU082) Supplementation Relieves Ulcerative Colitis by Affecting Intestinal Barrier Functions, Immunity-Related Gene Expression, Gut Microbiota, and Metabolic Pathways in Mice

Probiotics can effectively improve ulcerative colitis (UC), but the mechanism is still unclear. Here, shotgun metagenome and transcriptome analyses were performed to explore the therapeutic effect and the mechanism of the probiotic Lactobacillus plantarum HNU082 (Lp082) on UC. The results showed that Lp082 treatment significantly ameliorated dextran sulfate sodium (DSS)-induced UC in mice, which was manifested as increases in body weight, water intake, food intake, and colon length and decreases in disease activity index (DAI), immune organ index, inflammatory factors, and histopathological scores after Lp082 intake. An in-depth study discovered that Lp082 could improve the intestinal mucosal barrier and relieve inflammation by cooptimizing the biological barrier, chemical barrier, mechanical barrier, and immune barrier. Specifically, Lp082 rebuilt the biological barrier by regulating the intestinal microbiome and increasing the production of short-chain fatty acids (SCFAs). Lp082 improved the chemical barrier by reducing intercellular cell adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule (VCAM) and increasing goblet cells and mucin2. Lp082 ameliorated the mechanical barrier by increasing zonula occludens-1 (ZO-1), zonula occludens-2 (ZO-2), and occludin while decreasing claudin-1 and claudin-2. Lp082 optimized the immune barrier by reducing the content of interleukin-1β (IL-1β), IL-6, tumor necrosis factor-α (TNF-α), myeloperoxidase (MPO), and interferon-γ (IFN-γ) and increasing IL-10, transforming growth factor-β1 (TGF-β1), and TGF-β2, inhibiting the NF-κB signaling pathway. Taken together, probiotic Lp082 can play a protective role in a DSS-induced colitis mouse model by protecting the intestinal mucosal barrier, attenuating the inflammatory response, and regulating microbial imbalance. This study provides support for the development of probiotic-based microbial products as an alternative treatment strategy for UC. IMPORTANCE Many studies have focused on the therapeutic effect of probiotics on ulcerative colitis (UC), but few studies have paid attention to the mechanism of probiotics, especially the therapeutic effect. This study suggests that Lp082 has a therapeutic effect on colitis in mice. Its mechanisms of action include protecting the mucosal barrier and actively modulating the gut microbiome, modulating inflammatory pathways, and reducing neutrophil infiltration. Our study enriches the mechanism and provides a new prospect for probiotics in the treatment of colitis, helps to deepen the understanding of the intestinal mucosal barrier, and provides guidance for the future probiotic treatment of human colitis.

Phosphite treatment can improve root biomass and nutrition use efficiency in wheat

Phosphite represents a reduced form of phosphate that belongs to a class of crop growth-promoting chemicals termed biostimulants. Previous research has shown that phosphite application can enhance root growth, but its underlying mechanism, especially during environmental stresses, remains elusive. To uncover this, we undertook a series of morphological and physiological analyses under nutrient, water and heat stresses following a foliar application in wheat. Non-invasive 3D imaging of root system architecture directly in soil using X-ray Computed Tomography revealed that phosphite treatment improves root architectural traits and increased root biomass. Biochemical and physiological assays identified that phosphite treatment significantly increases Nitrate Reductase (NR) activity, leaf photosynthesis and stomatal conductance, suggesting improved Nitrogen and Carbon assimilation, respectively. These differences were more pronounced under heat or drought treatment (photosynthesis and photosystem II stability) and nutrient deficiency (root traits and NR). Overall our results suggest that phosphite treatment improves the ability of plants to tolerate abiotic stresses through improved Nitrogen and Carbon assimilation, combined with improved root growth which may improve biomass and yield.

Fermented Brewers’ Spent Grain Containing Dextran and Oligosaccharides as Ingredient for Composite Wheat Bread and Its Impact on Gut Metabolome In Vitro

Brewers’ spent grain or BSG is a fiber and protein rich food-grade side stream that has remained underutilized due to its poor technological and sensory characteristics. In this study, BSG was fermented with Weissella confusa A16 in presence of sucrose to induce the synthesis of dextran and maltosyl-isomaltooligosaccharides. Fermented BSG with or without the above polysaccharides was used as ingredient in wheat bread. Digestion of BSG breads was simulated in vitro with Simulator of Human Intestinal Microbial Ecosystem, and levels of fecal metabolites were analyzed. Enrichment of BSG breads with in situ dextran and maltosyl-isomaltooligosaccharides improved the baking quality compared to native BSG. Metabolism of free amino acids and synthesis of short chain fatty acids varied at different stages and parts of colon. The increase in butyric acid was similar in both the proximal and distal colon. In situ dextran and maltosyl-isomaltooligosaccharides, and higher content of proteins and fiber in BSG breads had a positive influence towards gut microbiota functionality. Along with several essential amino acids, an increase in amount of γ-aminobutyric acid was also observed after simulated digestion. BSG breads had a significant effect on the gut metabolome during in vitro digestion, showing increased production of microbial metabolites with potential health benefits.

How Microbiome Composition Correlates with Biochemical Changes during Sauerkraut Fermentation: a Focus on Neglected Bacterial Players and Functionalities

This study provided a new perspective on the bacterial community succession during sauerkraut fermentation, and on resulting metabolic functions. While culture-dependent methods confirmed the key role of the well-known core microbiome species, metagenomic approach (shotgun) revealed Secundilactobacillus malefermentans as a species of the core microbiome, especially during the last weeks of fermentation. Although the potentiality of S. malefermentans has not yet fully explored, it held core functional genes usually attributed to others lactic acid bacteria driving sauerkraut fermentation. Based on our results it is arguable that S. malefermentans might have a key a role during sauerkraut fermentation carried out at low temperature. Under our experimental conditions, the profile of phenolic compounds changed throughout sauerkraut fermentation. The amount of free phenolics, including free phenolic acids, increased at the beginning of the fermentation, whereas the conversion of phenolic acids into microbial derivatives was consistent during the last part of the sauerkraut fermentation. We pioneered correlating changes in the phenolics profile to changes in the microbiome, although the framework presented is still fragmentary. Annotated genes linked to the phenolic compounds metabolism (VprA and padA) were found in many core species during the whole process. A high metabolic potential for phenolics bioconversion emerged for lactobacilli and Pediococcus spp. through correlation analysis between microbiome composition and phenolics profile.

IMPORTANCE Our study was not limited to describe the succession pattern of the microbial community during sauerkraut fermentation, but also revealed how some neglected bacterial players belong to the core species during sauerkrauts processing, especially at low temperature. Such species might have a role as potential starters to optimize the fermentation processes and to obtain sauerkrauts with improved and standardized nutritional and sensory features. Furthermore, our correlations between microbiome composition and phenolics profile might also represent new references for sauerkraut biotechnology, aiming to identify new metabolic drivers of potential sauerkraut functionalities. Finally, sauerkraut ecosystem is a tractable model, although with high level of complexity, and resultant ecological information might be extended to other plant ecosystems.

Genetic Diversity and Environmental Influence on Yield and Yield-Related Traits of Adzuki Bean (Vigna angularis L.)

Adzuki beans are an important food legume crop in East Asia. A large number of adzuki bean accessions are maintained in the Chinese national seed genebank. A collection of 59 elite cultivars, 389 landraces, and 27 wild adzuki beans were selected and phenotyped extensively for yield and yield-related traits at two different locations (Nanning and Nanyang, China). Ten agronomic and yield-related traits were scored, and the data were subjected to analysis of variance (ANOVA), principal component analysis (PCA), correlation, and cluster analysis. Significant variation was observed for genotypes, locations, and genotype x environment interaction for most traits. Also, there were significant differences in the phenotypes among accessions of different germplasm types. The broad-sense heritability of traits studied ranged from 4.4% to 77.8%. The number of seeds per pod (77.8%), 100-seed weight (68.0%), and number of plant branches (63.9%) had a high heritability. A total of 10 traits were transformed into 3 comprehensive factors by principal component analysis, and the first three principal component factors contributed 72.31% of the total variability. Cluster analysis categorized the 475 adzuki bean accessions into five distinct groups. The results described in this study will be useful for adzuki bean breeders for the development of varieties with high end-use quality.

LPIN1 Is a Regulatory Factor Associated With Immune Response and Inflammation in Sepsis

Objectives

Sepsis is a clinical disease that is typically treated in the intensive care unit, and the complex pathophysiology under this disease has not been thoroughly understood. While ferroptosis is involved in inflammation and infection, its effect in sepsis is still unknown. The study aimed to identify ferroptosis-related genes in sepsis, providing translational potential therapeutic targets.

Methods

The dataset GSE65682 was used to download the sample source from the Gene Expression Omnibus (GEO) database. Consensus weighted gene co-expression network analysis (WGCNA) was performed to find suspected modules of sepsis. The differentially expressed genes (DEGs) most significantly associated with mortality were intersected with those altered by lipopolysaccharide (LPS) treatment and were further analyzed for the identification of main pathways of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The related pathway markers were further verified by qPCR.

Results

A total of 802 blood samples with sepsis were included for WGCNA, which identified 21 modules. Intersected with ferroptosis databases and LPS treatment groups, we identified two ferroptosis-related genes: PEBP1 and LPIN1. Only LPIN1 contributes to a poor outcome. Then, 205 DEGs were further identified according to the high or low LPIN1 expression. Among them, we constructed a gene regulatory network with several transcriptional factors using the NetworkAnalyst online tool and identified that these genes mostly correlate with inflammation and immune response. The immune infiltration analysis showed that lower expression of LPIN1 was related to macrophage infiltration and could be an independent predictor factor of the survival status in sepsis patients. Meanwhile, the multivariate Cox analysis showed that LPIN1 had a significant correlation with survival that was further verified by in vitro and in vivo experiments.

Conclusion

In conclusion, LPIN1 could become a reliable biomarker for patient survival in sepsis, which is associated with immune and inflammation status.

Constructing a Defined Starter for Multispecies Vinegar Fermentation via Evaluating the Vitality and Dominance of Functional Microbes in Autochthonous Starter

Mature vinegar culture has usually been used as a type of autochthonous starter for rapidly initiate initiating the next batch of acetic acid fermentation (AAF) and maintaining the batch-to-batch uniformity of AAF in the production of traditional cereal vinegar. However, the vitality and dominance of functional microbes in autochthonous starters remain unclear, which hinders further improvement of fermentation yield and production. Here, based on metagenomic (MG), metatranscriptomic (MT), and 16S rRNA gene sequencings, 11 bacterial operational taxonomic units (OTUs) with significant metabolic activity (MT/MG ratio >1) and dominance (relative abundance >1%) were targeted in the autochthonous vinegar starter, all of which were assigned to 4 species (Acetobacter pasteurianus, Lactobacillus acetotolerans, L. helveticus, Acetilactobacillus jinshanensis). Then, we evaluated the successions and interactions of these 11 bacterial OTUs at different AAF stages. Last, a defined starter was constructed with 4 core species isolated from the autochthonous starter (A. pasteurianus, L. acetotolerans, L. helveticus, Ac. jinshanensis). The defined starter culture could rapidly initiate the AAF in a sterile or unsterilized environment and similar dynamics of metabolites (ethanol, titratable acidity, acetic acid, lactic acid, and volatile compounds) and environmental indexes (temperature, pH) of fermentation were observed as compared with that of autochthonous starter (P > 0.05). This work provides a method to construct a defined microbiota from a complex system while preserving its metabolic function. IMPORTANCE Complex microorganisms are beneficial to the flavor formation in natural food fermentation, but they also pose challenges to the mass production of standardized products. It is attractive to construct a defined starter to rapidly initiate fermentation process and significantly improve fermentation yield. This study provides a comprehensive understanding of vital and dominant species in the autochthonous vinegar starter via multi-omics, and designs a defined microbial community for the efficient fermentation of cereal vinegar.

Gene and prognostic value of N6-methyladenosine (m6A) modification regulatory factors in lung adenocarcinoma

Lung cancer is the leading cause of death worldwide, and its incidence continues to increase. The treatment of lung cancer is related to the subtypes and stages of cancer, but the therapeutic effect is still unsatisfactory. We found that 10 of the 13 genes were differentially expressed in lung cancer, YTHDF1, RBM15, HNRNPC, KIAA1429, METTL3 and YTHDF2 are high expression while METTL14, ZC3H13, FTO and WTAP are low expression. HNRNPC and METTL3 genes were associated with the risk and prognosis of LUAD and could regard as biomarkers for early diagnosis and treatment, which provides a theoretical basis for LUAD.

Genetic structure analyses and ancestral information inference of Chinese Kyrgyz group via a panel of 39 AIM-DIPs

Ancestry informative markers have extensive uses and advantages in inferring ancestral origins and estimating ancestral genetic information components of admixed populations. With the characteristics of highly cultural exchange and the admixed genetic structure of the Kyrgyz group, it is essential to enrich the genetic data of the Kyrgyz group. In this study, we used a self-developed ancestry informative marker-deletion/insertion polymorphic (AIM-DIP) panel to explore ancestral components of Chinese Kyrgyz group and population genetic relationships between the Kyrgyz group and reference populations. Results showed that all AIM-DIP loci were conformed to Hardy-Weinberg equilibrium. There were 36 AIM-DIP loci that contributed significantly to genetic information inference. Multiple statistical analyses revealed that Chinese Kyrgyz group had a closer genetic relationship with Chinese Uyghur group. The ancestral components of the Kyrgyz group, being mostly composed of genetic components of European and East Asian populations, were more similar to the ancestral components of Chinese Uyghur group.

Physicochemical, flavor and microbial dynamic changes during low-salt doubanjiang (broad bean paste) fermentation

This study aimed to elaborate the roles of salt concentration on doubanjiang (broad bean paste) fermentation. Three sets of doubanjiang samples which had lower salt concentration than commercial doubanjiang were prepared and the physicochemical parameters, biogenic amines, flavor, microbial dynamics were analyzed during fermentation. The salt reduction showed significant effect on the dynamics of bacteria and fungi, thus leading to doubanjiang samples with different properties. Salt reduction during fermentation relieved the osmotic pressure towards microbes, which favored the accumulation of amino acid nitrogen, amino acids, and volatile flavor compounds. However, higher concentrations of total acids and biogenic amines and the existence of conditional pathogens, such as Klebsiella, Cronobacter and Acinetobacter genera, were observed in salt reduced doubanjiang samples, which was undesirable for doubanjiang quality. This study would deep our understanding of the roles of salt on doubanjiang fermentation.

Rapid temperature responses of photosystem II efficiency forecast genotypic variation in rice vegetative heat tolerance

A key target for the improvement of Oryza sativa (rice) is the development of heat-tolerant varieties. This necessitates the development of high-throughput methodologies for the screening of heat tolerance. Progress has been made to this end via visual scoring and chlorophyll fluorescence; however, these approaches demand large infrastructural investments to expose large populations of adult plants to heat stress. To address this bottleneck, we investigated the response of the maximum quantum efficiency of photosystem II (PSII) to rapidly increasing temperatures in excised leaf segments of juvenile rice plants. Segmented models explained the majority of the observed variation in response. Coefficients from these models, i.e. critical temperature (T_crit ) and the initial response (m₁ ), were evaluated for their usability for forecasting adult heat tolerance, measured as the vegetative heat tolerance of adult rice plants through visual (stay-green) and chlorophyll fluorescence (ɸPSII) approaches. We detected substantial variation in heat tolerance of a randomly selected set of indica rice varieties. Both T_crit and m₁ were associated with measured heat tolerance in adult plants, highlighting their usability as high-throughput proxies. Variation in heat tolerance was associated with daytime respiration but not with photosynthetic capacity, highlighting a role for the non-photorespiratory release of CO₂ in heat tolerance. To date, this represents the first published instance of genetic variation in these key gas-exchange traits being quantified in response to heat stress in a diverse set of rice accessions. These results outline an efficient strategy for screening heat tolerance and accentuate the need to focus on reduced rates of respiration to improve heat tolerance in rice.

Visualizing Multiple Variables Across Scale and Geography

Comparing multiple variables to select those that effectively characterize complex entities is important in a wide variety of domains - geodemographics for example. Identifying variables that correlate is a common practice to remove redundancy, but correlation varies across space, with scale and over time, and the frequently used global statistics hide potentially important differentiating local variation. For more comprehensive and robust insights into multivariate relations, these local correlations need to be assessed through various means of defining locality. We explore the geography of this issue, and use novel interactive visualization to identify interdependencies in multivariate data sets to support geographically informed multivariate analysis. We offer terminology for considering scale and locality, visual techniques for establishing the effects of scale on correlation and a theoretical framework through which variation in geographic correlation with scale and locality are addressed explicitly. Prototype software demonstrates how these contributions act together. These techniques enable multiple variables and their geographic characteristics to be considered concurrently as we extend visual parameter space analysis (vPSA) to the spatial domain. We find variable correlations to be sensitive to scale and geography to varying degrees in the context of energy-based geodemographics. This sensitivity depends upon the calculation of locality as well as the geographical and statistical structure of the variable.