scholarly journals Plant Developmental Stage Drives the Differentiation in Ecological Role of Plant Bacterial and Fungal Microbiomes

2021 ◽  
Author(s):  
Chao Xiong ◽  
Brajesh K. Singh ◽  
Ji-Zheng He ◽  
Yan-Lai Han ◽  
Pei-Pei Li ◽  
...  
Keyword(s):  
Developmental Stage ◽  
Plant Development ◽  
Late Stage ◽  
Developmental Stages ◽  
Early Stage ◽  
Alpha Diversity ◽  
Microbial Interactions ◽  
Disease Suppression ◽  
Fungal Communities ◽  
Ecological Role

Abstract BackgroundPlants live with diverse microbial communities which profoundly affect multiple facets of host performance such as nutrition acquisition, disease suppression and productivity, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils (rhizosphere and bulk soil), plant epiphytic and endophytic niches (phylloplane, rhizoplane, leaf and root endosphere), and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics.ResultsOur results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartment niches than in soils, with the strongest effect in the phylloplane. Air (represented by fake plants) was an important source of phylloplane microbiomes which were co-shaped by both plant development and seasonal environmental factors. Further, we demonstrated that bacterial and fungal communities in plant compartment niches exhibited contrasting response to host developmental stages, with higher alpha diversity and stronger deterministic assembly within bacterial microbiomes at the early stage but a similar pattern within mycobiomes at the late stage. Moreover, we found that bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity and functional genes involved in nutrient provision and disease resistance at the early stage than the late stage. ConclusionsOur results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different plant development stages. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection to meet the physiological requirement of plant developmental stages. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity.

scholarly journals Plant developmental stage drives the differentiation in ecological role of the maize microbiome

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Chao Xiong ◽  
Brajesh K. Singh ◽  
Ji-Zheng He ◽  
Yan-Lai Han ◽  
Pei-Pei Li ◽  
...  
Keyword(s):  
Plant Growth ◽  
Developmental Stage ◽  
Late Stage ◽  
Developmental Stages ◽  
Early Stage ◽  
Microbial Interactions ◽  
Fungal Communities ◽  
Ecological Role ◽  
N Assimilation ◽  
Deterministic Processes

Abstract Background Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics. Results Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage. Conclusions Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity.

scholarly journals The Effect of Amanita rubescens Pers Developmental Stages on Aroma Profile

2021 ◽  
Vol 7 (8) ◽  
pp. 611
Author(s):  
Jana Štefániková ◽  
Patrícia Martišová ◽  
Marek Šnirc ◽  
Vladimír Kunca ◽  
Július Árvay
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
Developmental Stage ◽  
Volatile Compounds ◽  
Developmental Stages ◽  
Early Stage ◽  
High Ratio ◽  
Gas Chromatography Mass Spectrometry ◽  
Mature Stage ◽  
Aroma Profile

The dichloromethane extraction was applied to extracted volatile compounds of the six developmental stages of caps and stipes of an Amanita rubescens mushroom and the relative contents were measured with the gas chromatography-mass spectrometry. The number of identified compounds ranged between 53 and 52, respectively, with a high ratio of alkane volatiles. The significant differences between the aroma compounds were determined in caps to identify their stages of development. The fully mature stage caps were characterized by 4,6-dimethyl-dodecane (7.69 ± 1.15%), 2-hexyl-1-decanol (11.8 ± 1.61%), 1,3-di-tert-butylbenzene (11.4 ± 1.25%), heptadecyl pentadecafluorooctanoate (2.16 ± 0.31%), and 2-hexyl-1-dodecanol (13.5 ± 1.33%). Niacinamide (3.90 ± 0.07%) and glycerol (3.62 ± 1.27%) was present in the caps in the early-stage of the rotting mushroom, which represented the 10th–12th day of fructification. The caps and stipes from the 12th–15th day of fructification were characterized by 2,3-butanediol (11.7 ± 0.13% and 8.00 ± 0.10%, respectively). Moreover, the caps from this developmental stage were characterized by 2-methyl- and 3-methyl butanoic acids (0.18 ± 0.03% and 0.33 ± 0.02%, respectively) which are typical for the rotting stage. In this study, we confirmed the effect of A. rubescens developmental stages on the aroma profile.

Developmental Stage-Specific Microbiota Profile of a Polyphagous Fly

2019 ◽  
Author(s):  
Jack Horlick ◽  
Rajib Majumder ◽  
Ida Lundbäck ◽  
Phillip W. Taylor ◽  
Fleur Ponton ◽  
...  
Keyword(s):  
Developmental Stage ◽  
Relative Abundance ◽  
Developmental Stages ◽  
Life Stage ◽  
Alpha Diversity ◽  
Fruit Fly ◽  
Functional Relationships ◽  
Trade Offs ◽  
Microbiome Profile ◽  
Insect Fitness

Gut bacteria play a key role in insect fitness, but the changes in gut microbiome profile across developmental stages of holometabolous insects remains little explored. Understanding changes in the microbiome across life stages is an important step toward understanding the associated shifts in functional relationships and trade-offs. Here, we characterised the microbiome of larvae, pupae, and adults of the highly polyphagous fruit fly Bactrocera tryoni (Froggatt) (Diptera: Tephritidae) using next-generation sequencing. We sampled individuals from colonies that had been recently introduced to the laboratory environment from naturally infested fruits at generations one (‘G1’) and five (‘G5’). Alpha diversity increased across developmental stages at both G1 and G5, with maximum diversity in adults. Community composition changed across developmental stages and between generations. In G1, larval and pupal microbiomes were dominated by the genus Asaia whereas adult microbiomes were dominated by Enterobacter. In G5, larval and pupal microbiomes contained a high relative abundance of Asaia, but pupae also had a high relative abundance of Staphylococcus and Burkholderia, and there were no dominant patterns in adults. Our findings provide insights into the developmental stage-dependent microbiome associations of a polyphagous fly, and how host-symbiont interactions change at each life stage through the transition from nature to laboratory environments.

scholarly journals Multi-organ analysis of low-level somatic mosaicism reveals stage- and tissue-specific mutational features in human development

2021 ◽  
Author(s):  
Hyeonju Son ◽  
Ja Hye Kim ◽  
Il Bin Kim ◽  
Myeong-Heui Kim ◽  
Nam Suk Sim ◽  
...  
Keyword(s):  
Late Stage ◽  
Somatic Mutations ◽  
Developmental Stages ◽  
Early Stage ◽  
Somatic Mosaicism ◽  
Read Depth ◽  
Brain Regions ◽  
Cell Type Specificity ◽  
Mutational Signatures ◽  
Low Level

Most somatic mutations arising during normal development present as low-level in single or multiple tissues depending on the developmental stage and affected organs1-4. However, it remains unclear how the human developmental stages or mutation-carrying organs affect somatic mutations’ features. Here, we performed a systemic and comprehensive analysis of low-level somatic mutations using deep whole-exome sequencing (WES; average read depth: ∼500×) of 498 multiple organ tissues with matched controls from 190 individuals. We found that early-stage mutations shared between multiple organs are lower in number but showed higher allele frequencies than late-stage mutations [0.54 vs. 5.83 variants per individual: 6.17% vs. 1.5% variant allele frequency (VAF)] along with less nonsynonymous mutations and lower functional impacts. Additionally, early- and late-stage mutations had unique mutational signatures distinct from tumor-originate mutations. Compared with early-stage mutations presenting a clock-like signature across all studied organs or tissues, late-stage mutations show organ, tissue, and cell-type specificity in mutation count, VAFs, and mutational signatures. In particular, analysis of brain somatic mutations shows bimodal occurrence and temporal-lobe-specific mutational signatures. These findings provide new insight into the features of somatic mosaicisms dependent on developmental stages and brain regions.

scholarly journals Making the Grade during Pandemic: Early-stage and Late-stage Provisional Institutions

2021 ◽  
pp. 073112142110286
Author(s):  
Alexander B. Kinney ◽  
Nicholas J. Rowland
Keyword(s):  
Late Stage ◽  
Early Stage ◽  
State University ◽  
Institutional Work ◽  
Traditional Grading ◽  
Grading Policy ◽  
Temporary Solution ◽  
Rural State ◽  
Empirical Implications ◽  
Common Understanding

This is an article that draws on the institutional work literature about provisional institutions. To date, nearly every U.S. sector has been impacted by COVID-19. To sustain their core missions, highly institutionalized organizations such as universities have had to rethink foundational structures and policies. Using a historical ethnographic approach to investigate records from faculty senate deliberations at “Rural State University” (RSU), the authors examine the implementation of a temporary grading policy to supplement traditional, qualitative grades spring 2020 during the outbreak. The authors find that RSU implemented a temporary, supplemental grading policy as a provisional institution to momentarily supersede traditional grading as a means to—as soon as possible—return to it. This finding contrasts with the common understanding that provisional institutions operate primarily as a temporary solution to a social problem that leads to more stable and enduring, ostensibly nonprovisional institutions. The temporary grading policy, the authors argue, constitutes a “late-stage” provisional institution and, with this new lens, subsequently characterize the more commonplace understanding of provisional institutions as “early-stage.” This contribution has theoretical implications for studies of institutions and empirical implications for research on shared governance and disruption in higher education.

scholarly journals Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuping Li ◽  
Xiaoju Liang ◽  
Xuguo Zhou ◽  
Yu An ◽  
Ming Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stage ◽  
Reference Genes ◽  
Developmental Stages ◽  
Individual Factors ◽  
Congeneric Species ◽  
Spatio Temporal ◽  
The Stability ◽  
Different Tissues ◽  
Selection Of

AbstractGlycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.

Health Insurance Status as a Predictor of Mode of Colon Cancer Detection but Not Stage at Diagnosis: Implications for Early Detection

2021 ◽  
pp. 003335492199917
Author(s):  
Lindsey A. Jones ◽  
Katherine C. Brewer ◽  
Leslie R. Carnahan ◽  
Jennifer A. Parsons ◽  
Blase N. Polite ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Health Insurance ◽  
Early Detection ◽  
Late Stage ◽  
Early Stage ◽  
Insurance Status ◽  
Stage At Diagnosis ◽  
Health Insurance Status ◽  
Percentage Point Increase ◽  
Point Increase

Objective For colon cancer patients, one goal of health insurance is to improve access to screening that leads to early detection, early-stage diagnosis, and polyp removal, all of which results in easier treatment and better outcomes. We examined associations among health insurance status, mode of detection (screen detection vs symptomatic presentation), and stage at diagnosis (early vs late) in a diverse sample of patients recently diagnosed with colon cancer from the Chicago metropolitan area. Methods Data came from the Colon Cancer Patterns of Care in Chicago study of racial and socioeconomic disparities in colon cancer screening, diagnosis, and care. We collected data from the medical records of non-Hispanic Black and non-Hispanic White patients aged ≥50 and diagnosed with colon cancer from October 2010 through January 2014 (N = 348). We used logistic regression with marginal standardization to model associations between health insurance status and study outcomes. Results After adjusting for age, race, sex, and socioeconomic status, being continuously insured 5 years before diagnosis and through diagnosis was associated with a 20 (95% CI, 8-33) percentage-point increase in prevalence of screen detection. Screen detection in turn was associated with a 15 (95% CI, 3-27) percentage-point increase in early-stage diagnosis; however, nearly half (47%; n = 54) of the 114 screen-detected patients were still diagnosed at late stage (stage 3 or 4). Health insurance status was not associated with earlier stage at diagnosis. Conclusions For health insurance to effectively shift stage at diagnosis, stronger associations are needed between health insurance and screening-related detection; between screening-related detection and early stage at diagnosis; or both. Findings also highlight the need to better understand factors contributing to late-stage colon cancer diagnosis despite screen detection.

scholarly journals EU FP7 research funding for an orphan drug (Orfadin®) and vaccine (Hep C) development: a success and a failure?

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
L. Schmidt ◽  
O. Sehic ◽  
C. Wild
Keyword(s):  
Hepatitis C ◽  
Late Stage ◽  
Research Funding ◽  
Early Stage ◽  
Basic Research ◽  
Pharmaceutical Products ◽  
Clinical Development ◽  
Clinical Indication ◽  
Market Authorisation ◽  
Risk Capital

Abstract Background We considered the extent of the contribution of publicly funded research to the late-stage clinical development of pharmaceuticals and medicinal products, based on the European Commission (EC) FP7 research funding programme. Using two EC FP7-HEALTH case study examples—representing two types of outcomes—we then estimated wider public and charitable research funding contributions. Methods Using the publicly available database of FP7-HEALTH funded projects, we identified awards relating to late-stage clinical development according to the systematic application of inclusion and exclusion criteria, classified them according to product type and clinical indication, and calculated total EC funding amounts. We then identified two case studies representing extreme outcomes: failure to proceed with the product (hepatitis C vaccine) and successful market authorisation (Orfadin® for alkaptonuria). Total public and philanthropic research funding contributions to these products were then estimated using publicly available information on funding. Results 12.3% (120/977) of all EC FP7-HEALTH awards related to the funding of late-stage clinical research, totalling € 686,871,399. Pharmaceutical products and vaccines together accounted for 84% of these late-stage clinical development research awards and 70% of its funding. The hepatitis C vaccine received total European Community (FP7 and its predecessor, EC Framework VI) funding of €13,183,813; total public and charitable research funding for this product development was estimated at € 77,060,102. The industry sponsor does not consider further development of this product viable; this now represents public risk investment. FP7 funding for the late-stage development of Orfadin® for alkaptonuria was so important that the trials it funded formed the basis for market authorisation, but it is not clear whether the price of the treatment (over €20,000 per patient per year) adequately reflects the substantial public funding contribution. Conclusions Public and charitable research funding plays an essential role, not just in early stage basic research, but also in the late-stage clinical development of products prior to market authorisation. In addition, it provides risk capital for failed products. Within this context, we consider further discussions about a public return on investment and its reflection in pricing policies and decisions justified.

scholarly journals Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hangxia Jin ◽  
Xiaomin Yu ◽  
Qinghua Yang ◽  
Xujun Fu ◽  
Fengjie Yuan
Keyword(s):  
Developmental Stage ◽  
Phytic Acid ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Defense Mechanisms ◽  
Developmental Stages ◽  
Sucrose Metabolism ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

scholarly journals Context-Specific Efficacy of Apalutamide Therapy in Preclinical Models of Pten-Deficient Prostate Cancer

Cancers ◽  
2021 ◽  
Vol 13 (16) ◽  
pp. 3975
Author(s):  
Marco A. De Velasco ◽  
Yurie Kura ◽  
Naomi Ando ◽  
Noriko Sako ◽  
Eri Banno ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Antitumor Activity ◽  
Cancer Cells ◽  
Late Stage ◽  
Early Stage ◽  
Castration Resistant Prostate Cancer ◽  
Akt Inhibitor ◽  
Molecular Features ◽  
Context Specific

Significant improvements with apalutamide, a nonsteroidal antiandrogen used to treat patients suffering from advanced prostate cancer (PCa), have prompted evaluation for additional indications and therapeutic development with other agents; however, persistent androgen receptor (AR) signaling remains problematic. We used autochthonous mouse models of Pten-deficient PCa to examine the context-specific antitumor activity of apalutamide and profile its molecular responses. Overall, apalutamide showed potent antitumor activity in both early-stage and late-stage models of castration-naïve prostate cancer (CNPC). Molecular profiling by Western blot and immunohistochemistry associated persistent surviving cancer cells with upregulated AKT signaling. While apalutamide was ineffective in an early-stage model of castration-resistant prostate cancer (CRPC), it tended to prolong survival in late-stage CRPC. Molecular features associated with surviving cancer cells in CRPC included upregulated aberrant-AR, and phosphorylated S6 and proline-rich Akt substrate of 40 kDa (PRAS40). Strong synergy was observed with the pan-AKT inhibitor GSK690693 and apalutamide in vitro against the CNPC- and CRPC-derived cell lines and tended to improve the antitumor responses in CNPC but not CRPC in vivo. Upregulation of signal transducer and activator of transcription 3 (STAT3) and proviral insertion in murine-1 (PIM-1) were associated with combined apalutamide/GSK690693. Our findings show that apalutamide can attenuate Pten-deficient PCa in a context-specific manner and provides data that can be used to further study and, possibly, develop additional combinations with apalutamide.

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