Current Issues in Molecular Biology

747 KiB

Open AccessReview

by Nuruliarizki Shinta Pandupuspitasari, Faheem Ahmed Khan, Chun-Jie Huang, Xing Chen and ShuJun Zhang

Curr. Issues Mol. Biol. 2016, 20(1), 47-54; https://doi.org/10.21775/cimb.020.047 - 7 Jan 2016

Cited by 1 | Viewed by 681

Abstract

The emerging role of the TREMs (Triggering Receptors Expressed by Myeloid cells) family in inflammation makes it important to explore their molecular mechanisms governing key pathways in inflammatory diseases. The TREMs family interaction with microbial products make it a strong candidate to target inflammatory diseases and raises an important question of its potential as a useful target in inflammatory diseases caused by products other than microbes, for example psoriasis. The interaction of TREMs with various immune responses can be of key importance in handling inflammatory diseases. The well established interaction of TREM-1 with microbial products like LPS and the emerging interactions with products from different important diseases of brain, heart, lungs and skin demands its full investigation as a therapeutic target. The post translational modifications (PTMs) that might regulate the functions of genes are also discussed and its future potential is reviewed. Furthermore, Its close cross talk with TLRs, NLRs and NODs is also reviewed in context of developing novel therapeutics. Full article

633 KiB

Open AccessReview

Natural Attributes and Agricultural Implications of Somatic Genome Variation

by Xiu-Qing Li

Curr. Issues Mol. Biol. 2016, 20(1), 29-46; https://doi.org/10.21775/cimb.020.029 - 5 Dec 2015

Viewed by 573

Abstract

This article proposes the concept of genome network, describes different variations of the somatic genome network, and reviews the agricultural implications of such variations. All genetic materials in a cell constitute the genome network of the cell and can jointly influence the cell's function and fate. The somatic genome of a plant is the genome network of cells in somatic tissues and of nonreproductive cells in pollen and ovules. Somatic genome variation (SGV, approximately equivalent to somagenetic variation) occurs at multiple levels, including stoichiometric, ploidy, and sequence variations. For a multicellular organism, the term “somatic genome variation” covers both the variation in part of the organism and the generation of new genotype individuals through somatic means from a sexually produced original genotype. For unicellular organisms, genome variation in somatic nuclei occurs at the whole organism level because there is only a single cell per individual. Growth, development and evolution of living organisms require both stability and instability of their genomes. Somatic genome variation displays many more attributes than genetic mutation and has strong implications for agriculture. Full article

3168 KiB

Open AccessReview

Identification of Top-Ranked Proteins within a Directional Protein Interaction Network Using the PageRank Algorithm: Applications in Humans and Plants

by Xiu-Qing Li, Tim Xing and Donglei Du

Curr. Issues Mol. Biol. 2016, 20(1), 13-28; https://doi.org/10.21775/cimb.020.013 - 5 Dec 2015

Cited by 1 | Viewed by 643

Abstract

Somatic mutation of signal transduction genes or key nodes of the cellular protein network can cause severe diseases in humans but can sometimes genetically improve plants, likely because growth is determinate in animals but indeterminate in plants. This article reviews protein networks; human protein ranking; the mitogen-activated protein kinase (MAPK) and insulin (phospho-inositide 3kinase [PI3K]/phosphatase and tensin homolog [PTEN]/protein kinase B [AKT]) signaling pathways; human diseases caused by somatic mutations to the PI3K/PTEN/ AKT pathway; use of the MAPK pathway in plant molecular breeding; and protein domain evolution. Casitas B-lineage lymphoma (CBL), PTEN, MAPK1 and PIK3CA are among PIK3CA the top-ranked proteins in directional rankings. Eight proteins (ACVR1, CDC42, RAC1, RAF1, RHOA, TGFBR1, TRAF2, and TRAF6) are ranked in the top 50 key players in both signal emission and signal reception and in interaction with many other proteins. Top-ranked proteins likely have major impacts on the network function. Such proteins are targets for drug discovery, because their mutations are implicated in various cancers and overgrowth syndromes. Appropriately managing food intake may help reduce the growth of tumors or malformation of tissues. The role of the protein kinase C/fatty acid synthase pathway in fat deposition in PTEN/PI3K patients should be investigated. Both the MAPK and insulin signaling pathways exist in plants, and MAPK pathway engineering can improve plant tolerance to biotic and abiotic stresses such as salinity. Full article

2374 KiB

Open AccessReview

Keeping CRISPR/Cas On-Target

by Muhammad Jamal, Faheem Ahmed Khan, Lin Da, Zeshan Habib, Jinxia Dai and Gang Cao

Curr. Issues Mol. Biol. 2016, 20(1), 1-12; https://doi.org/10.21775/cimb.020.001 - 11 Oct 2015

Cited by 7 | Viewed by 776

Abstract

CRISPR/Cas, a microbial adaptive immune system, has recently been reshaped as a versatile genome editing approach, endowing genome engineering with high efficiency and robustness. The DNA endonuclease Cas, a component of CRISPR system, is directed to specific target within genomes by guide RNA (gRNA) and performs gene editing function. However, the system is still in its infancy and facing enormous challenges such as off-target mutation. Lots of attempts have been made to overcome such off-targeting and proven to be effective. In this review we focused on recent progress of increasing the CRISPR specificity realized by rational design of gRNA and modification of Cas9 endonuclease. Meanwhile the methods to screen off-target mutation and their effects are also discussed. Comprehensive consideration and rational design to reduce off-target mutation and selection of effective screening assay will greatly facilitate to achieve successful CRISPR/Cas system mediated gene editing. Full article

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Curr. Issues Mol. Biol., Volume 20, Issue 1 (July 2016) – 4 articles

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