Current Issues in Molecular Biology

2889 KiB

Open AccessReview

Allele Mining Strategies: Principles and Utilisation for Blast Resistance Genes in Rice (Oryza sativa L.)

by Sadegh Ashkani, Mohd Rafii Yusop, Mahmoodreza Shabanimofrad, Amin Azadi, Ali Ghasemzadeh, Parisa Azizi and Mohammad Abdul Latif

Curr. Issues Mol. Biol. 2015, 17(1), 57-74; https://doi.org/10.21775/cimb.017.057 - 23 Feb 2015

Cited by 4 | Viewed by 980

Abstract

Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these [...] Read more.

Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement. Full article

605 KiB

Open AccessReview

Inosine at Different Primer Positions to Study Structure and Diversity of Prokaryotic Populations

by Eitan Ben-Dov and Ariel Kushmaro

Curr. Issues Mol. Biol. 2015, 17(1), 53-56; https://doi.org/10.21775/cimb.017.053 - 20 Feb 2015

Cited by 2 | Viewed by 549

Abstract

Culture-independent methods, employed to study the diversity and complexity of microbial communities that are based on amplification of rRNA genes with universal primers, include gradient gel electrophoresis (denaturing or temperature), single-strand-conformation polymorphism, restriction fragment length polymorphism, qPCR and high-throughput DNA sequencing. Substituting one [...] Read more.

Culture-independent methods, employed to study the diversity and complexity of microbial communities that are based on amplification of rRNA genes with universal primers, include gradient gel electrophoresis (denaturing or temperature), single-strand-conformation polymorphism, restriction fragment length polymorphism, qPCR and high-throughput DNA sequencing. Substituting one or more base(s) within or at the 3'-termi of the universal primers by inosine can overcome some of their shortcomings improving amplification capacity. Universal primer sets do not usually amplify sequences with nucleotide mismatch to the templates, particularly in the last three bases, whereas inosine-modified primers anneal and amplify a variety of rRNA gene sequences. Inosine-containing primers are therefore might be useful to detect more species in diverse prokaryotic populations. The article summarizes the pros and cons of using inosine especially at the 3' termini of universal primers in nucleic acid amplification for the study of microbial diversity. Full article

1263 KiB

Open AccessReview

ADARs and the Balance Game between Virus Infection and Innate Immune Cell Response

by Sara Tomaselli, Federica Galeano, Franco Locatelli and Angela Gallo

Curr. Issues Mol. Biol. 2015, 17(1), 37-52; https://doi.org/10.21775/cimb.017.037 - 11 Dec 2014

Cited by 4 | Viewed by 674

Abstract

All viruses that have dsRNA structures at any stages of their life cycle may potentially undergo RNA editing events mediated by ADAR enzymes. Indeed, an increasing number of studies that describe A-to-I sequence changes in viral genomes and/or transcripts, consistent with ADAR deaminase [...] Read more.

All viruses that have dsRNA structures at any stages of their life cycle may potentially undergo RNA editing events mediated by ADAR enzymes. Indeed, an increasing number of studies that describe A-to-I sequence changes in viral genomes and/or transcripts, consistent with ADAR deaminase activity, has been reported so far. These modifications can appear as either hyperediting or specific RNA editing events in viral dsRNAs. It is now well established that ADAR enzymes can affect viral life cycles in an editing-dependent and -independent manner, with ADARs acting as pro- or anti-viral factors. Despite the discovery of editing events in viral RNAs dates back to thirty years ago, the biological consequences of A-to-I changes during viral infection is still far to be completely elucidated. In this review, past and recent studies on the importance of ADAR enzymes on several viruses will be examined. Full article

2864 KiB

Open AccessReview

Regulation of Ion Channel and Transporter Function Through RNA Editing

by Miguel Holmgren and Joshua J.C. Rosenthal

Curr. Issues Mol. Biol. 2015, 17(1), 23-36; https://doi.org/10.21775/cimb.017.023 - 27 Oct 2014

Cited by 1 | Viewed by 502

Abstract

A large proportion of the recoding events mediated by RNA editing are in mRNAs that encode ion channels and transporters. The effects of these events on protein function have been characterized in only a few cases. In even fewer instances are the mechanistic [...] Read more.

A large proportion of the recoding events mediated by RNA editing are in mRNAs that encode ion channels and transporters. The effects of these events on protein function have been characterized in only a few cases. In even fewer instances are the mechanistic underpinnings of these effects understood. This review focuses on how RNA editing affects protein function and higher order physiology. In mammals, particular attention is given to the GluA2, an ionotropic glutamate receptor subunit, and K_v 1.1, a voltage-dependent K⁺ channel, because they are particularly well understood. In K_v addition, work on cephalopod K⁺ channels and Na⁺/K⁺-ATPases has also provided important clues on the rules used by RNA editing to regulate excitability. Finally, we discuss some of the emerging targets for editing and how this process may be used to regulate nervous function in response to a variable environment. Full article

1051 KiB

Open AccessReview

Extended Spectrum Beta-lactamases: Definition, Classification and Epidemiology

by Sobhan Ghafourian, Nourkhoda Sadeghifard, Sara Soheili and Zamberi Sekawi

Curr. Issues Mol. Biol. 2015, 17(1), 11-22; https://doi.org/10.21775/cimb.017.011 - 12 May 2014

Cited by 21 | Viewed by 7952

Abstract

Extended spectrum beta-lactamases (ESBLs) are defined as enzymes produced by certain bacteria that are able to hydrolyze extended spectrum cephalosporin. They are therefore effective against beta-lactam antibiotics such as ceftazidime, ceftriaxone, cefotaxime and oxyimino-monobactam. The objective of the current review is to provide [...] Read more.

Extended spectrum beta-lactamases (ESBLs) are defined as enzymes produced by certain bacteria that are able to hydrolyze extended spectrum cephalosporin. They are therefore effective against beta-lactam antibiotics such as ceftazidime, ceftriaxone, cefotaxime and oxyimino-monobactam. The objective of the current review is to provide a better understanding of ESBL and the epidemiology of ESBL producing organisms which are among those responsible for antibiotic resistant strains. Globally, ESBLs are considered to be problematic, particularly in hospitalized patients. There is an increasing frequency of ESBL in different parts of the world. The high risk patients are those contaminated with ESBL producer strains as it renders treatment to be ineffective in these patients. Thus, there an immediate needs to identify EBSL and formulate strategic policy initiatives to reduce their prevalence. Full article

1577 KiB

Open AccessReview

SETDB1 in Early Embryos and Embryonic Stem Cells

by Yong-Kook Kang

Curr. Issues Mol. Biol. 2015, 17(1), 1-10; https://doi.org/10.21775/cimb.017.001 - 4 Apr 2014

Cited by 1 | Viewed by 650

Abstract

The histone methyltransferase SETDB1 contributes to the silencing of local chromatin and the target specificity appears to be determined through various proteins that SETDB1 interacts with. This fundamental function endows SETDB1 with specialized roles in embryonic cells. Keeping the genomic and transcriptomic integrity [...] Read more.

The histone methyltransferase SETDB1 contributes to the silencing of local chromatin and the target specificity appears to be determined through various proteins that SETDB1 interacts with. This fundamental function endows SETDB1 with specialized roles in embryonic cells. Keeping the genomic and transcriptomic integrity via proviral silencing and maintaining the pluripotency by repressing the differentiation-associated genes have been demonstrated as the roles of SETDB1 in embryonic stem cells. In early developing embryos, SETDB1 exhibits characteristic nuclear mobilizations that might account for its pleiotropic roles in these rapidly changing cells as well. Early lethality of SETDB1-null embryos, along with other immunolocalization findings, suggests that SETDB1 is necessary for reprogramming and preparing the genomes of zygotes and pluripotent cells for the post-implantation developmental program. Full article

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Curr. Issues Mol. Biol., Volume 17, Issue 1 (January 2015) – 6 articles

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