Article
Plant Sciences
Vitor Batista Pinto, Vinicius Costa Almeida, Italo A. Pereira-Lima, Ellen Moura Vale, Wagner L. Araujo, Vanildo Silveira, Jose Marcelo Soriano Viana
Summary: Al responsive proteins play a key role in carbohydrate metabolic pathways. Sucrose synthase may contribute to Al tolerance. Responses to Aluminum toxicity are regulated at transcriptional and post-transcriptional levels.
Article
Biochemistry & Molecular Biology
Victor D'Amico-Damiao, Ian C. Dodd, Reginaldo Oliveira, Jose C. B. Lucio, Davi R. Rossatto, Rogerio F. Carvalho
Summary: The cry1a mutant in tomato showed reduced root biomass and length, higher tissue malondialdehyde concentrations, and increased leaf relative water content (RWC) under water deficit conditions. Grafted plants exhibited shoot and root biomass accumulation mainly determined by scion genotype, with cry1a rootstocks increasing RWC and WT rootstocks maintaining photosynthesis of cry1a scions in drying soil. Manipulating tomato CRY1a may enhance plant drought tolerance by altering leaf pigmentation and gas exchange during soil drying via local and long-distance effects.
Article
Biochemistry & Molecular Biology
Laura Ceballos-Laita, Daisuke Takahashi, Matsuo Uemura, Javier Abadia, Ana Flor Lopez-Millan, Jorge Rodriguez-Celma
Summary: Iron and manganese are essential elements for plants, but they compete for the same uptake transporters and show conflicting interactions at the regulatory level. Proteomic techniques were used to study the proteome profiles of tomato roots grown under iron or manganese deficiency. The results showed that both deficiencies led to common cell wall remodelling, but differed greatly in terms of oxidative stress, coumarin production, protein, nitrogen, and energy metabolism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agronomy
Camilo Lopez-Cristoffanini, Mireia Bundo, Xavier Serrat, Blanca San Segundo, Marta Lopez-Carbonell, Salvador Nogues
Summary: Rice, a major staple and highly salt-sensitive cereal, exhibits different proteomic and physiological responses to salinity stress in roots and shoots, with roots showing a faster and more coordinated response. These findings suggest that roots play a critical role in the tolerance observed in cultivars harboring the major QTL for salinity tolerance, Saltol.
Article
Biochemical Research Methods
Robert Winkler
Summary: Comparing multiple label-free shotgun proteomics datasets requires various data processing steps, including peptide-spectrum matching, protein inference, and quantification. ProtyQuant is a tool that integrates data from multiple experiments, aiding in protein comparison and providing intuitive information on protein probability and quantity. The accumulated peptide probability (app) serves as a reliable measure of 'Protein Presence,' facilitating protein identification and quantification in comparative proteomics.
JOURNAL OF PROTEOMICS
(2021)
Review
Biochemistry & Molecular Biology
Muhammad Naeem, Zeeshan Ali, Anzal Khan, Sami-Ul-Allah, Hassan Javed Chaudhary, Javeria Ashraf, Faheem Shahzad Baloch
Summary: Rice, as a crucial food crop for half of the world population, has a small genome size and its whole sequenced genome has proven to be valuable for genome research. The sequenced rice genome provides insights into molecular biology, transcriptomics, and genetic variability, which are essential for improving yield, quality, and stress resistance in rice crop.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Chemistry, Applied
Rocio Galindo-Lujan, Laura Pont, Zoran Minic, Maxim V. Berezovski, Victoria Sanz-Nebot, Fernando Benavente
Summary: This study analyzed the proteins from different varieties of quinoa seeds from Peru and Bolivia using advanced LC-MS/MS technology, identifying protein similarities and differences in the proteome. The comprehensive experimental quinoa seed proteome map presented in this study serves as a valuable starting point for further characterization and nutritional studies of quinoa and quinoa-containing food products.
Article
Plant Sciences
Naqeebullah Kakar, Salah H. Jumaa, Saroj Kumar Sah, Edilberto D. Redona, Marilyn L. Warburton, Kambham R. Reddy
Summary: Drought stress is a significant factor limiting plant growth. The study evaluates the drought tolerance of 74 rice genotypes using specially designed mini-hoop structures. Different shoot and root traits were measured and analyzed. The results showed a wide range of variability among genotypes, with leaf area being the most significantly affected trait. Drought had a limited effect on root traits. The study highlights the importance of using root traits as better descriptors for drought tolerance screening.
Article
Plant Sciences
Shivani Saini, Navdeep Kaur, Deeksha Marothia, Baldev Singh, Varinder Singh, Pascal Gantet, Pratap Kumar Pati
Summary: The study revealed that the salt tolerant rice cultivar Luna Suvarna exhibited stress adaptive root traits and higher accumulation of auxin compared to the salt sensitive cultivar IR64. Luna Suvarna also showed increased levels of auxin homeostasis genes transcript under salinity stress, along with differential regulation of salinity stress responsive proteins in its roots, highlighting the morphological and molecular features that contribute to its salinity stress tolerance.
Article
Biochemistry & Molecular Biology
Han-Qing Wang, Xing -Yu Zhao, Wei Xuan, Peng Wang, Fang-Jie Zhao
Summary: Root developmental plasticity is crucial for plants to adapt to a changing soil environment. This study reveals that plants can sense and avoid heterogeneous abiotic stress in soil by rapidly proliferating lateral roots in stress-free areas. Reactive oxygen species and calcium signaling play important roles in this process, and a signaling cascade involving ROS, auxin, and cell wall remodeling promotes lateral root development.
Review
Plant Sciences
Bhaskar Sarma, Hamdy Kashtoh, Tensangmu Lama Tamang, Pranaba Nanda Bhattacharyya, Yugal Kishore Mohanta, Kwang-Hyun Baek, Antonio Scopa, Daniela Businelli
Summary: Rice, as one of the most significant staple foods worldwide, has faced challenges due to climate change and abiotic stress. Abiotic stressors such as drought, heat, cold, salt, submergence, and heavy metal toxicity have resulted in reduced photosynthetic efficiency, imbalanced redox homeostasis, and tissue damage in rice plants. Rice plants respond to these stressors through various morphological, biochemical, and physiological mechanisms.
Article
Plant Sciences
Jonaliza L. Siangliw, Burin Thunnom, Mignon A. Natividad, Marinell R. Quintana, Dmytro Chebotarov, Kenneth L. McNally, Jonathan P. Lynch, Kathleen M. Brown, Amelia Henry
Summary: This study examined the phenotypic and genetic correlations among root anatomical, morphological, and agronomic phenotypes in rice accessions from Southeast Asia under drought stress. The results identified root phenotypes related to productivity and revealed candidate genes associated with root development, providing useful information for genetic improvement.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Jenna E. Fonta, Jitender Giri, Phanchita Vejchasarn, Jonathan P. Lynch, Kathleen M. Brown
Summary: The anatomical and architectural phenotypes of rice roots were examined to understand their responses to drought stress. The study found that the plasticity of root phenotypes in Azucena contributes to its drought tolerance by reducing the metabolic cost of soil exploration and improving water transport efficiency.
Article
Biochemical Research Methods
Yao Zhu, Ruth M. Hamill, Anne Maria Mullen, Alan L. Kelly, Mohammed Gagaoua
Summary: The beef sensory quality is influenced by various factors such as the interaction between muscle physiology and environment. Omics studies have the potential to uncover the biological connections between proteome and phenotype, providing validation and new insights. In this study, multivariate analysis of proteome and meat quality data identified 85 proteins related to sensory traits. Regression models and biomarkers were developed to explain the variability of multiple beef quality traits.
JOURNAL OF PROTEOMICS
(2023)
Article
Biochemical Research Methods
Mohammad Arefian, Thottethodi Subrahmanya Keshava Prasad
Summary: This study characterized the early effects of salt stress on the proteome and metabolome of rice tissues. It identified numerous signaling pathways that were rapidly induced or partially induced by salt stress. Through a combined analysis, it revealed the most sensitive components of signaling pathways causing salt-susceptibility in rice and suggested potential targets for crop improvement.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Soumalya Sarkar, Vivek K. Gupta, Samridhi Sharma, Ting Shen, Veer Gupta, Mehdi Mirzaei, Stuart L. Graham, Nitin Chitranshi
Summary: Alterations in RXR signalling are associated with neurodegenerative disorders. This study identified deleterious SNPs that affect the structure and function of RXR isoforms. Seven missense mutations were found in RXR isoforms, including two novel mutations. In silico prediction tools were used to assess the pathogenicity and stability of RXR mutations. The analysis showed a mix of conclusive and inconclusive genotype-phenotype correlations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Neurosciences
Tee Jong Huat, Tessa Onraet, Judith Camats-Perna, Estella A. Newcombe, Kim C. Ngo, Ashley N. Sue, Mehdi Mirzaei, Frank M. LaFerla, Rodrigo Medeiros
Summary: This study reveals that MyD88 plays a pivotal role in the regulation of astrocyte response to Alzheimer's disease (AD), with upregulated expression in AD patients. Deletion of astrocytic MyD88 protects mice from acute synaptic toxicity and cognitive impairment caused by beta-amyloid. Loss of astrocytic MyD88 results in altered astrocyte reactivity, lower levels of immune-related proteins, and higher expression of synaptic-related proteins in response to beta-amyloid.
Article
Plant Sciences
Shima Sadat Beheshti Rooy, Mehdi Ghabooli, Ghasem Hosseini Salekdeh, Ehsan Mohseni Fard, Rouhollah Karimi, Masoud Fakhrfeshani, Mansour Gholami
Summary: This study evaluated the effects of cold stress on the expression of miRNAs in grapevine. It identified differentially expressed miRNAs and their target genes, which are mainly involved in the regulation of important transcription factors. Enrichment analysis revealed networks associated with responses to cold stress, providing valuable information for further research on miRNA-mediated cold stress tolerance in grapevines.
ACTA PHYSIOLOGIAE PLANTARUM
(2023)
Article
Plant Sciences
Zahra Ghorbanzadeh, Rasmieh Hamid, Feba Jacob, Mehdi Mirzaei, Mehrshad Zeinalabedini, Somayeh Abdirad, Brian J. Atwells, Paul A. A. Haynes, Mohammad Reza Ghaffari, Ghasem Hosseini Salekdeh
Summary: Root system architecture (RSA) plays a critical role in improving nutrient and water uptake and maintaining crop yield under both optimal and drought conditions. Sequencing of small RNAs in the meristematic root tips of rice genotypes Azucena and IR64 revealed changes in miRNA expression patterns under drought stress. Different target genes were predicted for the differentially expressed miRNAs (DEMs) in Azucena and IR64, suggesting distinct mechanisms for coping with drought stress. Azucena exhibited upregulation of miRNAs related to root elongation, root system development, and stress adaptation, while IR64 promoted thickening of cell walls for insulation purposes.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Clinical Neurology
Yosef Koronyo, Altan Rentsendorj, Nazanin Mirzaei, Giovanna C. Regis, Julia Sheyn, Haoshen Shi, Ernesto Barron, Galen Cook-Wiens, Anthony R. Rodriguez, Rodrigo Medeiros, Joao A. Paulo, Veer B. Gupta, Andrei A. Kramerov, Alexander V. Ljubimov, Jennifer E. Van Eyk, Stuart L. Graham, Vivek K. Gupta, John M. Ringman, David R. Hinton, Carol A. Miller, Keith L. Black, Antonino Cattaneo, Giovanni Meli, Mehdi Mirzaei, Dieu-Trang Fuchs, Maya Koronyo-Hamaoui
Summary: Pathologies of Alzheimer’s disease (AD) can be found in the neurosensory retina, but their exact nature and distribution in relation to disease progression in the brain are still largely unknown. This study conducted extensive histopathological and biochemical investigations of postmortem retina and brain tissues from 86 human donors to better understand the pathological features of AD in the retina. The findings suggest a quantitative relationship between retinopathy, brain pathology, and cognitive impairment, and may lead to the development of reliable retinal biomarkers for noninvasive screening and monitoring of AD.
ACTA NEUROPATHOLOGICA
(2023)
Article
Clinical Neurology
Haoshen Shi, Yosef Koronyo, Dieu-Trang Fuchs, Julia Sheyn, Ousman Jallow, Krishna Mandalia, Stuart L. Graham, Vivek K. Gupta, Mehdi Mirzaei, Andrei A. Kramerov, Alexander V. Ljubimov, Debra Hawes, Carol A. Miller, Keith L. Black, Roxana O. Carare, Maya Koronyo-Hamaoui
Summary: This study found that vascular amyloid beta (Aβ) protein deposits were detected in retinas of mild cognitively impaired (MCI) and Alzheimer's disease (AD) patients, and these deposits were linked to disease status. The study also revealed that the components of retinal vascular tight junctions (TJs) and Aβ expression were correlated with neuropathology. The severe decreases in retinal vascular zonula occludens-1 (ZO-1) and claudin-5 were identified in MCI and AD patients, which correlated with arteriolar Aβ(40) deposition and cerebral pathology and cognitive deficits.
ALZHEIMERS & DEMENTIA
(2023)
Article
Environmental Sciences
Shohreh Ariaeenejad, Kaveh Kavousi, Behrouz Zolfaghari, Swapnoneel Roy, Takeshi Koshiba, Ghasem Hosseini Salekdeh
Summary: A large amount of lignocellulosic waste is generated every day, which has severe environmental pollution effects. Using enzymes as biocatalysts for the degradation of lignocellulosic materials is a practical step towards green energy and environmental biosafety. The current study focuses on enzyme computationally screened from camel rumen metagenomics data with the capacity to degrade lignocellulosic-rich and recalcitrant materials.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Biotechnology & Applied Microbiology
Nitin Chitranshi, Rashi Rajput, Angela Godinez, Kanishka Pushpitha, Mehdi Mirzaei, Devaraj Basavarajappa, Veer Gupta, Samridhi Sharma, Yuyi You, Giovanna Galliciotti, Ghasem H. Salekdeh, Mark S. Baker, Stuart L. Graham, Vivek K. Gupta
Summary: Our research shows that oxidation deactivation impairs the inhibitory activity of the serine protease inhibitor neuroserpin (NS) in glaucoma. The loss of NS is detrimental to retinal structure and function, and perturbations in autophagy and microglial and synaptic markers are associated with NS ablation. On the other hand, upregulation of NS promotes retinal ganglion cell (RGC) survival and protects against glaucoma-induced degeneration.
Article
Agronomy
Yuki Tsujii, Baoli Fan, Brian J. Atwell, Hans Lambers, Zhangying Lei, Ian J. Wright
Summary: The allocation of leaf phosphorus (P) among different functions is coordinated with the leaf economic spectrum (LES) and plays a role in determining the co-occurrence of different species under P limitation. Pioneers exhibited higher total P concentration, particularly in fractions such as orthophosphate P (P-i), nucleic acid P (P-N) and lipid P (P-L), compared to non-pioneer species.
Article
Neurosciences
Faezeh Shekari, Morteza Abyadeh, Anna Meyfour, Mehdi Mirzaei, Nitin Chitranshi, Vivek Gupta, Stuart L. Graham, Ghasem Hosseini Salekdeh
Summary: A large number of people around the world suffer from visual impairment, and the available therapies focus on preventing the progression of eye disorders. This review explores the potential of using extracellular vesicles (EVs) as a regenerative therapy for eye-related complications. The review examines the current knowledge about EVs and their therapeutic applications, as well as the challenges in translating EV-based therapy into clinical settings.
PROGRESS IN NEUROBIOLOGY
(2023)
Article
Environmental Sciences
Shohreh Ariaeenejad, Kaveh Kavousi, Jian-Lin Han, Xue-Zhi Ding, Ghasem Hosseini Salekdeh
Summary: Enzymatic hydrolysis is a cheap and eco-friendly method for eliminating fatty substances from wastewater, and lipases can be utilized for bio-treatment of wastewater in various industrial applications. A novel stable lipase, PersiLipase1, was identified from tannery wastewater. It exhibited remarkable thermostability, maintained activity in a wide range of pH, and showed tolerance towards metal ions and organic solvents. The lipase demonstrated high efficiency in hydrolyzing olive oil and sheep fat, as well as in biotreatment of oil and grease from tannery wastewater.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biochemistry & Molecular Biology
Liting Deng, Vivek Gupta, Morteza Abyadeh, Nitin Chitranshi, Kanishka Pushpitha, Yunqi Wu, Veer Gupta, Yuyi You, Joao A. Paulo, Stuart L. Graham, Mehdi Mirzaei, Paul A. Haynes
Summary: Photoreceptor cells are highly vulnerable to oxidative stress, which plays a key role in ocular diseases leading to retinal degeneration and blindness. A mass-spectrometric study using TMT labelling revealed proteome changes in photoreceptor cells following oxidative stress induction. Differential expression of proteins involved in various pathways was observed in response to oxidative stress, including ECM receptor interaction, oxidative phosphorylation, and spliceosome pathways.
Article
Engineering, Environmental
Shohreh Ariaeenejad, Mahmood Barani, Mina Sarani, Azadeh Lohrasbi-Nejad, Ghasem Mohammadi-Nejad, Ghasem Hosseini Salekdeh
Summary: Efficient removal of toxic dyes from wastewater is crucial for environmental protection. In this study, a carrier matrix based on Co-doped NiO NPs was developed to improve the stability of laccase and achieve high removal efficiency of Azo dye-containing wastewater. The immobilized enzyme showed improved enzymatic activity and great potential for decolorization under broad pH and temperature ranges.
PROCESS SAFETY AND ENVIRONMENTAL PROTECTION
(2023)