Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis

Plant root symbiosis with Arbuscular mycorrhizal (AM) fungi improves uptake of water and mineral nutrients, improving plant development under stressful conditions. Unraveling the unified transcriptomic signature of a successful colonization provides a better understanding of symbiosis. We developed a framework for finding the transcriptomic signature of Arbuscular mycorrhiza colonization and its regulating transcription factors in roots of Medicago truncatula. Expression profiles of roots in response to AM species were collected from four separate studies and were combined by direct merging meta-analysis. Batch effect, the major concern in expression meta-analysis, was reduced by three normalization steps: Robust Multi-array Average algorithm, Z-standardization, and quartiling normalization. Then, expression profile of 33685 genes in 18 root samples of Medicago as numerical features, as well as study ID and Arbuscular mycorrhiza type as categorical features, were mined by seven models: RELIEF, UNCERTAINTY, GINI INDEX, Chi Squared, RULE, INFO GAIN, and INFO GAIN RATIO. In total, 73 genes selected by machine learning models were up-regulated in response to AM (Z-value difference > 0.5). Feature weighting models also documented that this signature is independent from study (batch) effect. The AM inoculation signature obtained was able to differentiate efficiently between AM inoculated and non-inoculated samples. The AP2 domain class transcription factor, GRAS family transcription factors, and cyclin-dependent kinase were among the highly expressed meta-genes identified in the signature. We found high correspondence between the AM colonization signature obtained in this study and independent RNA-seq experiments on AM colonization, validating the repeatability of the colonization signature. Promoter analysis of upregulated genes in the transcriptomic signature led to the key regulators of AM colonization, including the essential transcription factors for endosymbiosis establishment and development such as NF-YA factors. The approach developed in this study offers three distinct novel features: (I) it improves direct merging meta-analysis by integrating supervised machine learning models and normalization steps to reduce study-specific batch effects; (II) seven attribute weighting models assessed the suitability of each gene for the transcriptomic signature which contributes to robustness of the signature (III) the approach is justifiable, easy to apply, and useful in practice. Our integrative framework of meta-analysis, promoter analysis, and machine learning provides a foundation to reveal the transcriptomic signature and regulatory circuits governing Arbuscular mycorrhizal symbiosis and is transferable to the other biological settings

Pd nanocatalyst stabilized on amine-modified zeolite: Antibacterial and catalytic activities for environmental pollution remediation in aqueous medium

Baran, Talat ( Aksaray, Yazar ) Baran, Nuray Yılmaz ( Aksaray, Yazar )In this study, the immobilization of palladium nanoparticles (NPs) on amine modified zeolite (Zeo) particles bearing a heterocyclic ligand has been developed through immobilizing structurally defined furfural with long tail of 3-aminopropyltriethoxysilane. NH2 modified Zeo/Pd has been synthesized via facile multi-step organic amine functionalization as a sustainable, recoverable and highly active nanocatalyst in the reduction of hexavalent chromium [Cr(VI)], potassium hexacyanoferrate(III) (K3[Fe(CN)6]), 2,4-dinitrophenylhydrazine (2,4-DNPH), 4-nitrophenol (4-NP), Rhodamine B (RhB), Methylene Blue (MB) and Nigrosin (NS) at ambient temperature in aqueous media. The surface nature of zeolite was changed after NH2 modification, leading to a remarkable increase in the catalytic and antimicrobial performances. TEM and HRTEM (high resolution transmission electron microscopy), FESEM (field emission scanning electron microscopy), STEM (scanning transmission electron microscopy), TG-DTG (thermogravimetry/derivative thermogravimetry), FT-IR (Fourier transform infrared), XRD (X-ray diffraction), EDS (energy dispersive X-ray spectroscopy), elemental mapping, XPS (X-ray photoelectron spectroscopy) and Raman analyses have been used to characterize the as-prepared nanocatalyst. The high removal rates of these environmental pollutants with NH2 modified Zeo/Pd nanocatalyst (Pd NPs@Zeo) using sodium borohydride (NaBH4) and formic acid (HCOOH) at ambient temperature were measured via UV–Vis spectroscopy and the nanocatalyst could be reused at least eight times without any significant loss of catalytic activity

Palladium nanoparticles stabilized on a novel Schiff base modified Unye bentonite: Highly stable, reusable and efficient nanocatalyst for treating wastewater contaminants and inactivating pathogenic microbes

Baran, Nuray Yılmaz ( Aksaray, Yazar ) Baran, Talat ( Aksaray, Yazar )Efficient decoration and characterization of highly catalytic, active Pd nanoparticles (NPs) onto a novel Schiff base modified Unye bentonite (UN-Sch) with high coordination performance of structurally defined 2-pyrrolaldehyde ligands against palladium ions (Pd NPs@UN) have been described. Amine modified UN/Pd NPs were fabricated via a facile multi-step approach without utilizing any additional reducing agents. To check the applicability of the synthesized Pd NPs@UN as highly active nanocatalysts in water and wastewater treatment, the reduction of highly toxic compounds such as 4-nitrophenol (4-NP), hexavalent chromium [Cr(VI)], Rhodamine B (RhB), potassium hexacyanoferrate(III) (K3[Fe(CN)6]) and congo red (CR) at ambient temperature in eco-friendly media has been investigated. The surface nature of Unye bentonite was altered after modification, leading to notable increase in the catalytic properties. The ensuing Pd NPs@UN demonstrated superior catalytic prowess (100% conversion within a few seconds for the aforementioned pollutants), excellent stability (~4 months) and superior recyclability (~96% yield after seven successive cycles). Notably, the present procedure is a clean and green one in which aqueous sodium borohydride (NaBH4) or formic acid (HCOOH) are used as reducing agents in the absence of any toxic reductants. Moreover, the results showed that Pd NPs@UN was effective against fungi and bacteria

Facile synthesis of Pd nanoparticles supported on a novel Schiff base modified chitosan-kaolin: Antibacterial and catalytic activities in Sonogashira coupling reaction

*Baran, Talat ( Aksaray, Yazar ) *Yılmaz Baran, Nuray ( Aksaray, Yazar )The present work studies the Sonogashira coupling reaction (SCR) between aryl halides and acetylenes under aerobic conditions using the catalytic complex of Pd nanoparticles (NPs) supported on a novel Schiff base modified chitosan-kaolin (Pd NPs@CS-Kao) in ethanol solvent. The prepared catalyst was characterized by TEM, SEM, FT-IR, XRD, EDS, XPS, elemental mapping, and Raman analyses. The products were formed in high yields. At the end of the reaction, Pd NPs@CS-Kao can be filtered and reused for five consecutive cycles. The advantages of this catalytic process include simple methodology, high yields, and easy work-up. In addition, Pd NPs@CS-Kao exhibited effective antibacterial performance against E. coli gram-negative bacteria