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Current Issues in Molecular Biology is published by MDPI from Volume 43 Issue 1 (2021). Previous articles were published by another publisher in Open Access under a CC-BY (or CC-BY-NC-ND) licence, and they are hosted by MDPI on mdpi.com as a courtesy and upon agreement with Caister Press.

Curr. Issues Mol. Biol., Volume 19, Issue 1 (April 2016) – 13 articles

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930 KiB  
Review
Linking Biomarker and Comparative Omics to Pathogens in Legumes
by Marwan Diapari
Curr. Issues Mol. Biol. 2016, 19(1), 137-144; https://doi.org/10.21775/9781910190357.13 - 11 Sep 2015
Cited by 1 | Viewed by 358
Abstract
It is envisioned that a more precise study of the association between the traits and biomarkers will dramatically decrease the time and costs required to bring new improved disease resistance lines to market. The field of omics has an enormous potential to assess [...] Read more.
It is envisioned that a more precise study of the association between the traits and biomarkers will dramatically decrease the time and costs required to bring new improved disease resistance lines to market. The field of omics has an enormous potential to assess diseases more precise, including the identification and understanding of pathogenic mechanisms in legume crops, and have been exemplified by a relatively large number of studies. Recently, molecular genetic studies have accumulated a huge amount of genotypic data, through a more affordable next generation sequencing (NGS) technology, causing the omics approaches to fall behind. In this paper I provide an overview of genomics and proteomics and their use in legume crops, including the use of comparative genomics to identify homologous markers within legume crops. Full article
1374 KiB  
Review
An Overview of Proteomics Tools for Understanding Plant Defense Against Pathogens
by Carolina Grandellis, Cecilia V. Vranych, Ainelén Piazza, Betiana S. Garavaglia, Natalia Gottig and Jorgelina Ottado
Curr. Issues Mol. Biol. 2016, 19(1), 129-136; https://doi.org/10.21775/9781910190357.12 - 11 Sep 2015
Cited by 4 | Viewed by 445
Abstract
Plant diseases are responsible for important losses in crops and cause serious impacts in agricultural production. In the last years, proteomics has been used to examine plant defense responses against pathogens. Such studies may be pioneer in the generation of crops with enhanced [...] Read more.
Plant diseases are responsible for important losses in crops and cause serious impacts in agricultural production. In the last years, proteomics has been used to examine plant defense responses against pathogens. Such studies may be pioneer in the generation of crops with enhanced resistance. In this review, we focus on proteomics advances in the understanding of host and non-host resistance against pathogens. Full article
827 KiB  
Review
Transcriptomic Analyses on the Role of Nitric Oxide in Plant Disease Resistance
by Capilla Mata-Pérez, Juan C. Begara-Morales, Francisco Luque, María N. Padilla, Jaime Jiménez-Ruiz, Beatriz Sánchez-Calvo, Jesús Fierro-Risco and Juan B. Barroso
Curr. Issues Mol. Biol. 2016, 19(1), 121-128; https://doi.org/10.21775/9781910190357.11 - 11 Sep 2015
Cited by 4 | Viewed by 408
Abstract
Nitric oxide (NO) is a gaseous molecule having key roles in many physiological processes such as germination, growth, development and senescence. It has been also shown the important role of NO as a signaling molecule in the response to a wide variety of [...] Read more.
Nitric oxide (NO) is a gaseous molecule having key roles in many physiological processes such as germination, growth, development and senescence. It has been also shown the important role of NO as a signaling molecule in the response to a wide variety of stress situations, including both biotic and abiotic stress conditions. In the last few years, a growing number of studies have focused on NO-cell targets by several approaches such as transcriptomic and proteomic analyses. This review is centered on offering an update about the principal medium- and large-scale transcriptomic analyses performed with several NO donors including microarray, cDNA-amplification fragment length polymorphism (AFLP) and high throughput sequencing (RNA-seq technology) approaches mainly focused on the role of this reactive nitrogen species in relation to plant disease resistance. Different putative NO-responsive genes have been identified in different plant tissues and plant species by application of several NO donors suggesting the implication of NO-responsive genes with plant adaptive responses to biotic stress processes. Finally, it is also provided an overview about common transcription factor-binding sites of NO-responsive genes and the need to further analyze the different NO-targets by other omics studies. Full article
13549 KiB  
Review
Oscillating Transcriptome during Rice-Magnaporthe Interaction
by T.R. Sharma, Alok Das, Shallu Thakur, B.N. Devanna, Pankaj Kumar Singh, Priyanka Jain, Joshitha Vijayan and Shrawan Kumar
Curr. Issues Mol. Biol. 2016, 19(1), 99-120; https://doi.org/10.21775/9781910190357.10 - 11 Sep 2015
Cited by 10 | Viewed by 558
Abstract
Rice blast disease caused by the fungus, Magnaporthe oryzae, is one of the most devastating diseases of rice. Deciphering molecular mechanism of host-pathogen interactions is of great importance in devising disease management strategies. Transcription being the first step for gene regulation in [...] Read more.
Rice blast disease caused by the fungus, Magnaporthe oryzae, is one of the most devastating diseases of rice. Deciphering molecular mechanism of host-pathogen interactions is of great importance in devising disease management strategies. Transcription being the first step for gene regulation in eukaryotes, basic understanding of the transcriptome is sine qua non for devising effective management strategy. The availability of genome sequences of rice and M. oryzae has facilitated the process to a large extent. The current review summarizes recent understanding of rice-blast pathosystem, application of transcriptomics approaches to understand the interactions employing different platforms, major determinants in the interaction and possibility of using certain candidate for conditioning enhanced disease resistance (Effector Triggered Immunity and PAMP Triggered Immunity) and downstream signalling in rice. A better understanding of the interaction elements and effective strategies hold potential to reduce yield losses in rice caused by M. oryzae. Full article
1062 KiB  
Review
Omics Approaches for the Engineering of Pathogen Resistant Plants
by Diego F. Gomez-Casati, María A. Pagani, María V. Busi and Vijai Bhadauria
Curr. Issues Mol. Biol. 2016, 19(1), 89-98; https://doi.org/10.21775/9781910190357.09 - 11 Sep 2015
Cited by 14 | Viewed by 581
Abstract
The attack of different pathogens, such as bacteria, fungi and viruses has a negative impact on crop production. In counter such attacks, plants have developed different strategies involving the modification of gene expression, activation of several metabolic pathways and post-translational modification of proteins, [...] Read more.
The attack of different pathogens, such as bacteria, fungi and viruses has a negative impact on crop production. In counter such attacks, plants have developed different strategies involving the modification of gene expression, activation of several metabolic pathways and post-translational modification of proteins, which culminate into the accumulation of primary and secondary metabolites implicated in plant defense responses. The recent advancement in omics techniques allows the increase coverage of plants transcriptomes, proteomes and metabolomes during pathogen attack, and the modulation of the response after the infection. Omics techniques also allow us to learn more about the biological cycle of the pathogens in addition to the identification of novel virulence factors in pathogens and their host targets. Both approaches become important to decipher the mechanism underlying pathogen attacks and to develop strategies for improving disease-resistant plants. In this review, we summarize some of the contribution of genomics, transcriptomics, proteomics, metabolomics and metallomics in devising the strategies to obtain plants with increased resistance to pathogens. These approaches constitute important research tools in the development of new technologies for the protection against diseases and increase plant production. Full article
3093 KiB  
Review
RNAseq and Proteomics for Analysing Complex Oomycete Plant Interactions
by Dharani D. Burra, Ramesh R. Vetukuri, Svante Resjö, Laura J. Grenville-Briggs and Erik Andreasson
Curr. Issues Mol. Biol. 2016, 19(1), 73-88; https://doi.org/10.21775/9781910190357.08 - 11 Sep 2015
Cited by 4 | Viewed by 561
Abstract
The oomycetes include some of the most devastating plant pathogens. In this review we discuss the latest results from oomycete and plant studies with emphasis on interaction studies. We focus on the outcomes of RNAseq and proteomics studies and some pitfalls of these [...] Read more.
The oomycetes include some of the most devastating plant pathogens. In this review we discuss the latest results from oomycete and plant studies with emphasis on interaction studies. We focus on the outcomes of RNAseq and proteomics studies and some pitfalls of these approaches. Both pathogenic interactions and biological control are discussed. We underline the usefulness of studies at several levels of complexity from studies of one organism, up to two or more and within agricultural fields (managed settings) up to wild ecosystems. Finally we identify areas of future interest such as detailed interactome studies, dual RNAseq studies, peptide modification studies and population/meta omics with or without biological control agents. Full article
3396 KiB  
Review
The Power of Omics to Identify Plant Susceptibility Factors and to Study Resistance to Root-Knot Nematodes
by Javier Cabrera, Marta Barcala, Carmen Fenoll and Carolina Escobar
Curr. Issues Mol. Biol. 2016, 19(1), 53-72; https://doi.org/10.21775/9781910190357.07 - 11 Sep 2015
Cited by 10 | Viewed by 537
Abstract
Technology has contributed to the advances on the genomic, transcriptomic, metabolomic and proteomic analyses of the plant-root-knot nematode (RKN) interaction. Holistic approaches to obtain expression profiles, such as cDNA libraries, differential display, q-PCR, microarray hybridization, massive sequencing, etc., have increased our knowledge on [...] Read more.
Technology has contributed to the advances on the genomic, transcriptomic, metabolomic and proteomic analyses of the plant-root-knot nematode (RKN) interaction. Holistic approaches to obtain expression profiles, such as cDNA libraries, differential display, q-PCR, microarray hybridization, massive sequencing, etc., have increased our knowledge on the molecular aspects of the interaction and have triggered the development of biotechnological tools to control this plague. An important limitation, however, has been the difficulty of cross-comparative analysis of these data. The construction of a database, NEMATIC, compiling microarray data available in Arabidopsis of the interaction with plant endoparasitic nematodes facilitated the in silico analysis, but is not sufficient for the handling of 'omic' information of different plant species. Omics combined with cell isolation techniques have shed some light on the heterogeneous expression signatures of nematode induced gall tissues, i.e., plant defences are specifically inhibited in giant cells within the gall aiding the nematode for a successful establishment. The natural resistance against RKNs varies from an early hypersensitive reaction before the establishment of the nematode, to the arrest of gall growth. The molecular bases of these mechanisms, not fully understood yet, could disclose powerful targets for the development of biotechnology based tools for nematode control. Full article
13498 KiB  
Review
Rice Responses and Resistance to Planthopper-Borne Viruses at Transcriptomic and Proteomic Levels
by Feng Cui, Wan Zhao, Lan Luo and Le Kang
Curr. Issues Mol. Biol. 2016, 19(1), 43-52; https://doi.org/10.21775/9781910190357.06 - 11 Sep 2015
Cited by 9 | Viewed by 616
Abstract
Rice (Oryza sativa) is one of the most important cereal crops in the world, especially in Asian areas. Rice virus diseases are considered as the most serious threat to rice yields. Most rice viruses are transmitted by hemipteran insects such as [...] Read more.
Rice (Oryza sativa) is one of the most important cereal crops in the world, especially in Asian areas. Rice virus diseases are considered as the most serious threat to rice yields. Most rice viruses are transmitted by hemipteran insects such as planthoppers and leafhoppers. In Asia five rice viruses are transmitted mainly by three planthopper species in a persistent manner: Rice stripe virus, Rice black-streaked dwarf virus, Rice ragged stunt virus, Rice grassy stunt virus, and Southern rice black-streaked dwarf virus. In rice antivirus studies, several individual genes have been shown to function in rice resistance to viruses. Since plant responses to viral infection are complex, system-level omic studies are required to fully understand the responses. Recently more and more omic studies have appeared in the literatures on relationships between planthoppers and viruses, employing microarray, RNA-Seq, small RNA deep sequencing, degradome sequencing, and proteomic analysis. In this paper, we review the current knowledge and progress of omic studies in rice plant responses and resistance to four planthopper-borned viruses. We also discuss progress in the omic study of the interactions of planthoppers and rice viruses. Future research directions and translational applications of fundamental knowledge of virus-vector-rice interactions are proposed. Full article
946 KiB  
Review
Omics Approach to Identify Factors Involved in Brassica Disease Resistance
by Marta Francisco, Pilar Soengas, Pablo Velasco, Vijai Bhadauria, Maria E. Cartea and Victor M. Rodríguez
Curr. Issues Mol. Biol. 2016, 19(1), 31-42; https://doi.org/10.21775/9781910190357.05 - 11 Sep 2015
Cited by 8 | Viewed by 573
Abstract
Understanding plant's defense mechanisms and their response to biotic stresses is of fundamental meaning for the development of resistant crop varieties and more productive agriculture. The Brassica genus involves a large variety of economically important species and cultivars used as vegetable source, oilseeds, [...] Read more.
Understanding plant's defense mechanisms and their response to biotic stresses is of fundamental meaning for the development of resistant crop varieties and more productive agriculture. The Brassica genus involves a large variety of economically important species and cultivars used as vegetable source, oilseeds, forage and ornamental. Damage caused by pathogens attack affects negatively various aspects of plant growth, development, and crop productivity. Over the last few decades, advances in plant physiology, genetics, and molecular biology have greatly improved our understanding of plant responses to biotic stress conditions. In this regard, various 'omics' technologies enable qualitative and quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. In this review, we have described advances in 'omic' tools (genomics, transcriptomics, proteomics and metabolomics) in the view of conventional and modern approaches being used to elucidate the molecular mechanisms that underlie Brassica disease resistance. Full article
3241 KiB  
Review
Metabolomics of Disease Resistance in Crops
by Vicent Arbona and Aurelio Gómez-Cadenas
Curr. Issues Mol. Biol. 2016, 19(1), 13-30; https://doi.org/10.21775/9781910190357.04 - 11 Sep 2015
Cited by 33 | Viewed by 733
Abstract
Plants are continuously exposed to the attack of invasive microorganisms, such as fungi or bacteria, and also viruses. To fight these attackers, plants develop different metabolic and genetic responses whose final outcome is the production of either toxic compounds that kill the pathogen [...] Read more.
Plants are continuously exposed to the attack of invasive microorganisms, such as fungi or bacteria, and also viruses. To fight these attackers, plants develop different metabolic and genetic responses whose final outcome is the production of either toxic compounds that kill the pathogen or deter its growth, and/or semiotic molecules that alert other individuals from the same plant species. These molecules are derived from the secondary metabolism and their production is induced upon detection of a pathogen-associated molecular pattern (PAMP). These PAMPs are different molecules that are perceived by the host cell triggering defense responses. PAMP-elicited compounds are highly diverse and specific of every plant species and can be divided into preformed metabolites or phytoanticipins that are converted into toxic molecules upon pathogen perception, and toxic metabolites or phytoalexins that are produced only upon pathogen attack. Moreover, plant volatile emissions are also modified in response to pathogen attack to alert neighboring individuals or to make plants less attractive to pathogen vector arthropods. Plant metabolite profiling techniques have allowed the identification of novel antimicrobial molecules that are induced upon elicitation. However, more studies are required to assess the specific function of metabolites or metabolite blends on plant-microbe interactions. Full article
807 KiB  
Review
Current Status of Proteomic Studies on Defense Responses in Rice
by Xifeng Chen, Vijai Bhadauria and Bojun Ma
Curr. Issues Mol. Biol. 2016, 19(1), 7-12; https://doi.org/10.21775/9781910190357.03 - 11 Sep 2015
Cited by 1 | Viewed by 367
Abstract
Biotic stresses are constraints to plant growth and development negatively impacting crop production. To counter such stresses, plants have developed stress-specific adaptations as well as simultaneous responses. The efficacy and magnitude of inducible adaptive responses are dependent on activation of signaling pathways and [...] Read more.
Biotic stresses are constraints to plant growth and development negatively impacting crop production. To counter such stresses, plants have developed stress-specific adaptations as well as simultaneous responses. The efficacy and magnitude of inducible adaptive responses are dependent on activation of signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification of proteins associated with defense mechanisms. Proteomics plays an important role in elucidating plant defense mechanisms by mining the differential regulation of proteins to various biotic stresses. Rice, one of the most widely cultivated food crops in world, is constantly challenged by a variety of biotic stresses, and high-throughput proteomics approaches have been employed to unravel the molecular mechanism of the biotic stresses-response in rice. In this review, we summarize the latest advances of proteomic studies on defense responses and discuss the potential relevance of the proteins identified by proteomic means in rice defense mechanism. Furthermore, we provide perspective for proteomics in unraveling the molecular mechanism of rice immunity. Full article
1599 KiB  
Review
Wild Help for Enhancing Genetic Resistance in Lentil Against Fungal Diseases
by Vijai Bhadauria, Melissa M.L. Wong, Kirstin E. Bett and Sabine Banniza
Curr. Issues Mol. Biol. 2016, 19(1), 3-6; https://doi.org/10.21775/9781910190357.02 - 11 Sep 2015
Cited by 3 | Viewed by 322
Abstract
Lentil (Lens culinaris) is one of the cool season grain legume crops and an important source of dietary proteins and fibre. Fungal diseases are main constraints to lentil production and account for significant yield and quality losses. Lentil has a narrow [...] Read more.
Lentil (Lens culinaris) is one of the cool season grain legume crops and an important source of dietary proteins and fibre. Fungal diseases are main constraints to lentil production and account for significant yield and quality losses. Lentil has a narrow genetic base presumably due to a bottleneck during domestication and as a result, any resistance to fungal diseases in the cultivated genepool is gradually eroded and overcome by pathogens. New sources of resistance have been identified in wild lentil (Lens ervoides). This article provides an overview of harnessing resistance potential of wild germplasm to enhance genetic resistance in lentil cultivars using next-generation sequencing-based genotyping, comparative genomics and marker-assisted selection breeding. Full article
186 KiB  
Review
OMICS in Plant Disease Resistance
by Vijai Bhadauria
Curr. Issues Mol. Biol. 2016, 19(1), 1-2; https://doi.org/10.21775/9781910190357.01 - 11 Sep 2015
Cited by 6 | Viewed by 706
Abstract
The term OMICS, which look into the global profiling and analysis of various cellular molecules, has gained new heights with the advancement of next-generation sequencing and mass spectrometry technologies. It has broader implication in genetic improvement of crops for resistance against various diseases [...] Read more.
The term OMICS, which look into the global profiling and analysis of various cellular molecules, has gained new heights with the advancement of next-generation sequencing and mass spectrometry technologies. It has broader implication in genetic improvement of crops for resistance against various diseases of economic significance. This focus issue entitled OMICS in Plant Disease Resistance highlights the implication of OMICS (genomics, transcriptomics, proteomics and metabolomics) in agricultural research. Full article
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