Impact of model assumptions on the inference of the evolution of ectomycorrhizal symbiosis in fungi

Ectomycorrhiza (ECM) is a symbiotic relation between plant and fungi that is essential for nutrient uptake of many stand forming trees. There are two conflicting views about the evolution of ECM in fungi suggesting (1) relatively few transitions to ECM followed by reversals to non-ECM, or (2) many independent origins of ECM and no reversals. In this study, we compare these, and other, hypotheses and test the impact of different models on inference. We assembled a dataset of five marker gene sequences (nuc58, nucLSU, nucSSU, rpb1, and rpb2) and 2,174 fungal taxa covering the three subphyla: Agaricomycotina, Mucoromycotina and Pezizomycotina. The fit of different models, including models with variable rates in clades or through time, to the pattern of ECM fungal taxa was tested in a Bayesian framework, and using AIC and simulations. We find that models implementing variable rates are a better fit than models without rate shift, and that the conclusion about the relative rate between ECM and non-ECM depend largely on whether rate shifts are allowed or not. We conclude that standard constant-rate ancestral state reconstruction models are not adequate for the analysis of the evolution of ECM fungi, and may give contradictory results to more extensive analyses

Genetic modification of crop plants: issues and challenges

The growing area of genetically modified (GM) crops has significantly expanded since they were first commercialized in 1996. Currently 400 million acres of the fertile land worldwide are used to cultivate genetic engineering (GE) crops such as rice, corn, cotton, and soybeans. Genetically modified crops are increasingly gaining acceptance and their adoption has brought huge economic and environmental benefits. In the past 17 years, these achievements have been primarily supported by two simple traits of herbicide tolerant and insect resistant crops. Concurrently GM crops generated intense consumer debate in many parts of the world. The issues under debate include the costs and benefits of the GM crops and the inherent safety concerns. It is widely claimed, however, that biotechnology, particularly genetically engineered food offers dramatic promise for meeting some of the twenty-first century’s greatest challenges; as do all new technologies, it also poses certain apprehensions and risks, both known and unknown. The introduction of Bacillus thuringiensis (Bt) genes into the plants has raised issues related to its risk assessment and biosafety. The chapter presents an overview of the production of GM crops, their adequacy, detection strategies, biosafety issues, and potential impact on society. Furthermore, the future prospects of the GM crops are also highlighted

RAPD markers associated with salt tolerance in soybean genotypes under salt stress

In order to investigate the influence of genetic background on salt tolerance in soybean (Glycine max), ten soybean genotypes (Pusa-20, Pusa-40, Pusa-37, Pusa-16, Pusa-24, Pusa-22, BRAGG, PK-416, PK-1042, and DS-9712) released in India, were selected and grown hydroponically. The 10-day-old seedlings were subjected to 0, 25, 50, 75, 100, 125, and 150 mM NaCl for 15 days. Plant growth, leaf osmotic adjustment, and random amplified polymorphic DNA (RAPD) analysis were studied. In comparison to control plants, the plant growth in all genotypes was decreased by salt stress, respectively. Salt stress decreased leaf osmotic potential in all genotypes; however, the maximum reduction was observed in genotype Pusa-24 followed by PK-416 and Pusa-20, while minimum reduction was shown by genotype Pusa-37, followed by BRAGG and PK-1042. Pusa-16, Pusa-22, Pusa-40, and DS-9712 were able to tolerate NaCl treatment up to the level of 75 Mm. The difference in osmotic adjustment between all the genotypes was correlated with the concentrations of ion examined such as Na+ and the leaf proline concentration. These results suggest that the genotypic variation for salt tolerance can be partially accounted by plant physiological measures. Twenty RAPD primers revealed high polymorphism and genetic variation among ten soybean genotypes studied. The closer varieties in the cluster behaved similarly in their response to salinity tolerance. Intra-clustering within the two clusters precisely grouped the ten genotypes in sub-cluster as expected from their physiological findings. Our study shows that RAPD technique is a sensitive, precise, and efficient tool for genomic analysis in soybean genotypes

The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE

Background: The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level. Results: We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up-or down-regulated (> 3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress. Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na(+) homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available. Conclusions: This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms

Effect of different levels of EDTA on phytoextraction of heavy metal and growth of Brassica juncea L.

Heavy metal pollution of soil is a major concern due to its non-biodegradable nature, bioaccumulation, and persistence in the environment. To explore the probable function of EDTA in ameliorating heavy metal toxicity and achieve the sustainable development goal (SDG), Brassica juncea L. seedlings were treated with different concentrations of EDTA (0, 1.0, 2.0, 3.0, and 4.0 mM Kg−1) in heavy metal-polluted soil. Plant samples were collected 60 days after sowing; photosynthetic pigments, H2O2, monoaldehyde (MDA), antioxidant enzymes, and ascorbic acid content, as well as plant biomass, were estimated in plants. Soil and plant samples were also examined for the concentrations of Cd, Cr, Pb, and Hg. Moreover, values of the phytoremediation factor were utilized to assess the accumulation capacity of heavy metals by B. juncea under EDTA treatments. In the absence of EDTA, B. juncea seedlings accrued heavy metals in their roots and shoots in a concentration-dependent manner. However, the highest biomass of plants (roots and shoots) was recorded with the application of 2 mM kg−1 EDTA. Moreover, high levels (above 3 mM kg−1) of EDTA concentration have reduced the biomass of plants (roots and shoots), photosynthetic area, and chlorophyll content. The effect of EDTA levels on photosynthetic pigments (chlorophyll a and b) revealed that with an increment in EDTA concentration, accumulation of heavy metals was also increased in the plant, subsequently decreasing the chlorophyll a and b concentration in the plant. TLF was found to be in the order Pb> Hg> Zn> and >Ni, while TF was found to be in the order Hg>Zn>Ni>Pb, and the best dose was 3 mM kg−1 EDTA for Hg and 4 mM kg−1 for Pb, Ni, and Zn. Furthermore, hyperaccumulation of heavy metals enhanced the generation of hydrogen peroxide (H2O2), superoxide anions (O2•−), and lipid peroxidation. It also interrupts mechanisms of the antioxidant defense system. Furthermore, heavy metal stress reduced plant growth, biomass, and chlorophyll (chl) content. These findings suggest that the exogenous addition of EDTA to the heavy metal-treated seedlings increases the bioavailability of heavy metals for phytoextraction and decreases heavy metal-induced oxidative injuries by restricting heavy metal uptake and components of their antioxidant defense systems

Brassinosteroids as promoters of seedling growth and antioxidant activity under heavy metal zinc stress in mung bean (Vigna radiata L.)

The escalation of harmful pollutants, including heavy metals, due to industrialization and urbanization has become a global concern. To mitigate the negative impacts of heavy metal stress on germination and early plant development, growth regulators have been employed. This study aimed to evaluate the response of mung bean (Vigna radiata L.) to zinc stress in the presence of brassinosteroids, focusing on seedling growth and antioxidant potential. Mung bean seedlings were treated with three concentrations of 24-epibrassinolide (EBL) (0.1, 0.2, and 0.4 PPM) with or without zinc. Results demonstrated that the application of brassinosteroids, combined with zinc stress, significantly enhanced germination percentage (about 47.06, 63.64, and 120%), speed of germination (about 39.13, 50, and 100%), seedling growth (about 38% in case of treatment combined 0.4 PPM 24-EBL and 1.5 mM ZnSO4) and seedling vigor index (204% in case of treatment combined 0.4 PPM 24-EBL and 1.5 mM ZnSO4) compared to zinc-treated seedlings alone after 24 h. The activities of antioxidative enzymes (catalase, ascorbate peroxidase, polyphenol oxidase, and peroxidase) and total soluble protein content decreased, while lipid peroxidation and proline content exhibited a significant increase (p ≤ 0.05) when compared to the control. However, the negative effects induced by heavy metal stress on these parameters were significantly mitigated by EBL application. Notably, the most effective concentration of EBL in overcoming zinc stress was found to be 0.4 PPM. These findings underscore the potential of exogenously applied brassinosteroids as a valuable tool in phytoremediation projects by ameliorating heavy metal stress

Fruiting body form, not nutritional mode, is the major driver of diversification in mushroom-forming fungi

With ∼36,000 described species, Agaricomycetes are among the most successful groups of Fungi. Agaricomycetes display great diversity in fruiting body forms and nutritional modes. Most have pileate-stipitate fruiting bodies (with a cap and stalk), but the group also contains crust-like resupinate fungi, polypores, coral fungi, and gasteroid forms (e.g., puffballs and stinkhorns). Some Agaricomycetes enter into ectomycorrhizal symbioses with plants, while others are decayers (saprotrophs) or pathogens. We constructed a megaphylogeny of 8,400 species and used it to test the following five hypotheses regarding the evolution of morphological and ecological traits in Agaricomycetes and their impact on diversification: 1) resupinate forms are plesiomorphic, 2) pileate-stipitate forms promote diversification, 3) the evolution of gasteroid forms is irreversible, 4) the ectomycorrhizal (ECM) symbiosis promotes diversification, and 5) the evolution of ECM symbiosis is irreversible. The ancestor of Agaricomycetes was a saprotroph with a resupinate fruiting body. There have been 462 transitions in the examined morphologies, including 123 origins of gasteroid forms. Reversals of gasteroid forms are highly unlikely but cannot be rejected. Pileate-stipitate forms are correlated with elevated diversification rates, suggesting that this morphological trait is a key to the success of Agaricomycetes. ECM symbioses have evolved 36 times in Agaricomycetes, with several transformations to parasitism. Across the entire 8,400-species phylogeny, diversification rates of ectomycorrhizal lineages are no greater than those of saprotrophic lineages. However, some ECM lineages have elevated diversification rates compared to their non-ECM sister clades, suggesting that the evolution of symbioses may act as a key innovation at local phylogenetic scales

Health disparities between Black Hispanic and Black non-Hispanic cervical cancer cases in the USA

Background: Globally, cervical cancer is a major public health concern. Cervical cancer is the second most common cancer among women, resulting in approximately 500,000 cases per year. The purpose of this study is to compare disease characteristics between Black Hispanic (BH) and Black non-Hispanic (BNH) women in the US. Materials and Methods: We used stratified random sampling to select cervical cancer patient records from the SEER database (1973-2009). We used Chi-square and independent samples t-test to examine differences in proportions and means. Results: The sample included 2,000 cervical cancer cases of Black non-Hispanic and 91 Black Hispanic women. There were statistically significant differences between black Hispanic and black non- Hispanics in mean age at diagnosis (p\u3c0.001), mean survival time (p\u3c0.001), marital status (p\u3c0.001), primary site of cancer (p\u3c0.001); lymph node involvement (p\u3c0.001); grading and differentiation (p\u3c0.0001); and tumor behavior (p\u3c0.001). Black women were more likely to develop cervical cancer and to have the highest mortality rates from the disease. Conclusions: Findings from this study show clear racial and ethnic disparities in cervical cancer incidence and prognosis that should be addressed

Disparities in cervical cancer characteristics and survival between white Hispanics and white non-Hispanic women

Background:Cervical cancer is the second most common cancer among women resulting in nearly 500,000cases annually. Screening leads to better treatment and survival time. However, human papillomavirus (HPV)exposure, screening, and treatment vary among races and ethnicities in the United States. The purpose of thisstudy is to examine disparities in characteristics of cervical cancer and survival of cases between White Hispanic(WH) and White non-Hispanic (WNH) women in the United States.Methods:We used a stratified random sampling method to select cervical cancer patient records from ninestates; a simple random sampling method to extract the demographic and disease characteristics data withinstates from the Surveillance Epidemiology and End Results (SEER) database. We used statistical probabilitydistribution methods for discrete and continuous data. The chi-square test and independent samplest-testwere used to evaluate statistically significant differences. Furthermore, the Cox Proportional Regression andthe Kaplan–Meier survival estimators were used to compare WH and WNH population survival times in theUnited States.Results:The samples of WNH and WH women included 4,000 cervical cancer cases from 1973–2009. Therewere statistically significant differences between ethnicities: marital status (p\u3c0.001); primary site of cancer(p\u3c0.001); lymph node involvement (p\u3c0.001); grading and differentiation (p\u3c0.0001); and tumor behavior(p\u3c0.001). The mean age of diagnosis for both groups showed no statistical differences. However, the meansurvival time for WNH was 221.7 (standard deviation [SD]=118.1) months and for WH was 190.3 (SD=120.3),which differed significantly (p\u3c0.001).Conclusions:Clear disparities exist in risk factors, cervical cancer characteristics, and survival time betweenWH and WNH women

Pelargonium graveolens L., (Geranium) essential oil from Northeast India: chemical composition, pharmacology and genotoxicity study

Pelargonium graveolens L., essential oil (EO) has various therapeutic properties, including aromatherapy. The present experiment was designed to investigate chemical makeup of the P. graveolens (Geranium) EO from Northeast India using gas chromatography-mass spectroscopy (GC-MS) and gas chromatography-flame ionization detection (GC-FID), and the pharmacological potential was determined using a range of assays along with Allium cepa assay for genotoxicity study. GC-MS analysis of the EO revealed the presence of 11 compounds with a total 97.43% identified area, with citronellol (32.84%), geraniol (23.62%), and citronellyl formate (12.14%) as the major compounds. The essential oil exhibited type-II anti-diabetic properties with an IC50 6.66 μL/mL and skin whitening potential IC50 of 1.89 μL/mL. P. graveolens EO (IC50 26.16 μL/mL) was found to possess comparatively weaker anti-inflammatory agent than the standard diclofenac (IC50 9.24 μL/mL) in the protease inhibitory test. The EO demonstrated moderate antioxidant activity with an IC50 value of 22.68 μL/mL than ascorbic acid IC50 12.53 μL/mL in the ABTS assay. The EO was found to moderately affect the mitotic index (15.32%) and induce chromosomal aberrations (11.40%) at a concentration of 1 μL/mL after 72 h of exposure. Based on the findings the Northeast Indian variety of P. graveolens EO exhibits promising type-II anti-diabetic and skin whitening properties, which could be further utilized in the formulation of anti-diabetic and skin whitening agents after validation through clinical trials