https://www.cell.com/trends/microbiology/pdf/S0966-842X(08)00038-3.pdf

Bacillus lipopeptides: versatile weapons for plant disease biocontrol.

Heavy metal (HM) toxicity is one of the major abiotic stresses leading to hazardous effects in plants. A common consequence of HM toxicity is the excessive accumulation of reactive oxygen species (ROS) and methylglyoxal (MG), both of which can cause peroxidation of lipids, oxidation of protein, inactivation of enzymes, DNA damage and/or interact with other vital constituents of plant cells. Higher plants have evolved a sophisticated antioxidant defense system and a glyoxalase system to scavenge ROS and MG. In addition, HMs that enter the cell may be sequestered by amino acids, organic acids, glutathione (GSH), or by specific metal-binding ligands. Being a central molecule of both the antioxidant defense system and the glyoxalase system, GSH is involved in both direct and indirect control of ROS and MG and their reaction products in plant cells, thus protecting the plant from HM-induced oxidative damage. Recent plant molecular studies have shown that GSH by itself and its metabolizing enzymes—notably glutathione S-transferase, glutathione peroxidase, dehydroascorbate reductase, glutathione reductase, glyoxalase I and glyoxalase II—act additively and coordinately for efficient protection against ROS- and MG-induced damage in addition to detoxification, complexation, chelation and compartmentation of HMs. The aim of this review is to integrate a recent understanding of physiological and biochemical mechanisms of HM-induced plant stress response and tolerance based on the findings of current plant molecular biology research.

https://downloads.hindawi.com/archive/2012/872875.pdf

Molecular Mechanism of Heavy Metal Toxicity and Tolerance in Plants: Central Role of Glutathione in Detoxification of Reactive Oxygen Species and Methylglyoxal and in Heavy Metal Chelation

In a persistently changing environment, plants are constantly challenged by various abiotic stresses such as salinity, drought, temperature extremes, heavy metal toxicity, high-light intensity, nutrient deficiency, UV-B radiation, ozone, etc. which cause substantial losses in the yield and quality of a crop. A key sign of such stresses at the molecular level is the accelerated production of reactive oxygen species (ROS) such as singlet oxygen (1O2), superoxide (O2•−), hydrogen peroxide (H2O2) and hydroxyl radicals (OH•). ROS are extremely reactive in nature because they can interact with a number of cellular molecules and metabolites, thereby leading to irreparable metabolic dysfunction and death. Plants have well-developed enzymatic and non-enzymatic scavenging pathways or detoxification systems to counter the deleterious effects of ROS that include the enzymes superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), glutathione reductase (GR), glutathione S-transferase (GST), glutathione peroxidase (GPX) and peroxidases (POX) as well as non-enzymatic compounds such as ascorbate (AsA), glutathione (GSH), carotenoids and tocopherols. In plant cells, specific ROS-producing and scavenging systems are found in different organelles and the ROS-scavenging pathways from different cellular compartments are coordinated. Recent studies in plants have shown that relatively low levels of ROS act as signaling molecules that induce abiotic stress tolerance by regulating the expression of defense genes. Additionally, numerous results have shown that plants with higher levels of antioxidants, whether constitutive or induced, showed greater resistance to different types of environmental stresses. In this chapter we attempt to summarize recent researches on the mechanisms and possible regulatory roles of ROS in abiotic stress tolerance. Further, we discuss the progress made during the last few decades in improving the oxidative stress tolerance of plants through genetic engineering by different components of ROS detoxification systems in plants.

Plant Response and Tolerance to Abiotic Oxidative Stress: Antioxidant Defense Is a Key Factor

Medicago truncatula is a fast-emerging model for the study of legume functional biology. We used the tobacco retrotransposon Tnt1 to tag the Medicago genome and generated over 7600 independent lines representing an estimated 190,000 insertion events. Tnt1 inserted on average at 25 different locations per genome during tissue culture, and insertions were stable during subsequent generations in soil. Analysis of 2461 Tnt1 flanking sequence tags (FSTs) revealed that Tnt1 appears to prefer gene-rich regions. The proportion of Tnt1 insertion in coding sequences was 34.1%, compared to the expected 15.9% if random insertions were to occur. However, Tnt1 showed neither unique target site specificity nor strong insertion hot spots, although some genes were more frequently tagged than others. Forward-genetic screening of 3237 R(1) lines resulted in identification of visible mutant phenotypes in approximately 30% of the regenerated lines. Tagging efficiency appears to be high, as all of the 20 mutants examined so far were found to be tagged. Taking the properties of Tnt1 into account and assuming 1.7 kb for the average M. truncatula gene size, we estimate that approximately 14,000-16,000 lines would be sufficient for 90% gene tagging coverage in M. truncatula. This is in contrast to more than 500,000 lines required to achieve the same saturation level using T-DNA tagging. Our data demonstrate that Tnt1 is an efficient insertional mutagen in M. truncatula, and could be a primary choice for other plant species with large genomes.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2008.03418.x

Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula

Plant cell and tissue cultures can be established routinely under sterile conditions from explants, such as plant leaves, stems, roots, meristems etc for both the ways for multiplication and extraction of secondary metabolites. Strain improvement, methods for the selection of high-producing cell lines, and medium optimizations can lead to an enhancement in secondary metabolite production. However, most often trials with plant cell cultures fail to produce the desired products. In such cases, strategies to improve the production of secondary metabolites must be considered. One of the main problems encountered is the lack of basic knowledge of the biosynthetic routes, and mechanisms responsible for the production of plant metabolites. Where the productivity of the desired metabolites is limited by the lack of particular precursors, biotransformation using an exogenous supply of biosynthetic precursors, genetic manipulation and metabolic engineering may improve the accumulation of compounds. Feedback inhibition of metabolic enzymes as well as inhibition of membrane transport can be eliminated by the accumulation of synthesized products in a second phase introduced into the aqueous medium. Organ cultures and in vitro biomass production often have sites of synthesis and storage of secondary metabolites in separate compartments. Elicitors, compounds triggering the formation of secondary metabolites, can be abiotic or biotic. Natural elicitors include polysaccharides such as pectin and chitosan, which are also used in the immobilization and permeabilization of plant cells. Immobilization with suitable bioreactor system provides several advantages, such as continuous process operation, but for the development of an immobilized plant cell culture process, natural or artifically induced secretion of the accumulated product into the surrounding medium is necessary. The present review highlights the nature, applications, perspective and scale up methods for the production of valuable secondary metabolites in vitro.

	 

	Key words: Plant cell cultures, secondary metabolites, biotransformation, biosynthetic pathways, elicitation, immobilization, bioreactors.

/pdf/a-review-on-trends-in-production-of-secondary-metabolites-1i9vvpbtmc.pdf

A review on trends in production of secondary metabolites from higher plants by in vitro tissue, organ and cell cultures.

Floriculture, ornamental and plant biotechnology : advances and topical issues

ORCID (Open Researcher and Contributor ID) was launched in 2012 as an initiative to fortify the validity and integrity of academic publishing through author name disambiguation Less than a decade later, this portal is being actively promoted in an attempt to ensure that academics adhere to this permanent identifier Without a doubt, a complete, up-to-date and authentic ORCID has value, not only to a researcher, but to the academic community because it allows facilitated online submissions, and links to funding agencies and other profiles The mandatory requirement of an ORCID account for the submitting or corresponding author, sometimes for all authors, is becoming more common during the submission of manuscripts to ORCID member journals Not only are there issues pertaining to academic freedom, or unfair treatment of those without an ORCID, there are other highly pertinent, unpalatable, and contentious issues related to ORCID that need greater attention and debate These include the inconsistent implementation of ORCID among co-authors, the existence of empty or “ghost” ORCID accounts that are uninformative and thus of limited use, and the plausible abuse of ORCIDs to register potentially fake elements These issues would not only reduce trust in ORCID, which is actively promoted as a tool for maintaining science’s integrity, they may land up weakening a publishing system that was meant to be fortified by this initiative They may also hurt the reputation of valid ORCID users who share a platform with “ghost” ORCID accounts or with fake authors, or authors whose identities are unverifiable

http://nopr.niscair.res.in/bitstream/123456789/55973/1/ALIS%2067%284%29%20246-250.pdf

ORCID: Issues and concerns about its use for academic purposes and research integrity

In academic publishing, stings appear to be on the rise. Stings may involve a paper with nonsense or fabricated content, fictitious authors or affiliations, and may be supported by artificially created emails or ORCID accounts, the latter to offer a false impression of validation. In recent times, stings have been used to protest editorial policies or to challenge claims of peer review, with the objective of exposing flawed policies and procedures. While some hail stings as success stories in exposing poor editorial policies and publication flaws, and while others draw humor from them, very few academics have suprisingly assessed the ethics (or lack thereof) and/or criminality of such operations. Consequently, it is rare to find academic papers that are critical of such stings from an ethical and/or criminal perspective. An equally surprising fact is that ethics-promoting organizations (COPE, ICMJE, CSE), which have ethics guidelines for paper submission to a wide swathe of academic and scholarly journals and publishers, do not have ethics clauses specifically calling out sting operations, even though several of their stated ethics guidelines consider fake, false or falsified elements in an academic paper to be unethical. In this paper, some reflection on broad ethical, humor-related and possible criminal elements of sting operations in academic publishing are considered. In addition, the COPE, ICMJE and CSE ethics guidelines were scrutinized to identify any clauses that could support the argument that stings in academic publishing are unethical.

Assessing the Ethics of Stings, Including from the Prism of Guidelines by Ethics-Promoting Organizations (COPE, ICMJE, CSE)

Outsourced English revision, editing, publication consultation, and integrity services should be acknowledged in an academic paper

Science is in crisis: a crisis of trust, and a crisis of values. Yet, this is an opportune moment for scientists to examine the issues that underly science to discover how they may be of use, beyond their laboratory or field experience, to improve the research and publishing landscapes to create an environment that suits their needs more. Traditionally, the science publishing landscape had been controlled by the science, technology and medicine publishers, who have always taunted their peer review systems as being fail-safe. Yet, considerable moss has been gathered by the post-publication peer review (PPPR) movement over the past few years, indicating that the voice of the average scientist now carries more weight, and more value, than ever before. Despite this, most scientists are unaware of their potential power of opinion. Especially when it comes to commenting on, and correcting, the already published literature. Commenting by name, or anonymously, is the new PPPR publishing reality. There needs to also be a concomitant movement away from artificial metrics, such as the impact factor, which serve only as ego-boosting parameters, and which distract the wider readership from the weaknesses of the traditional peer review system currently in place. Increasing cases of the abuse of peer review, such as the creation of fake identities, affiliations or e-mail addresses further highlights the need for scientists to be vigilant, without necessairly being vigilantes. The discovery, within a matter of years, that the literature is more corrupted than was previously thought, in some cases caused by clear cases of editorial cronyism, or abuse, has resulted in a need for scientists to exceed their functions as mere scientists to evolve into whistle-blowers. Some ethical guidelines are in place, such as those by COPE, yet what is being increasingly witnessed, is a discrepancy between preached values by select COPE member journals, and the literature that they have published. Authorship issues continue to be plagued by inconsistencies in the application and verification of the ICMJE’s definitions. In a bid to expand their publishing options, open access has also reached a crisis with wave upon wave of 1 The author was at the Faculty of Agriculture, Kagawa University under various positions between 1997 and 2013, where he retired at the end of March, 2013. The author currently holds no teaching or editorial position, and is not affiliated with any publisher, journal or academic institute and is now an independent, free-lance scientist, science writer and consultant. Address for Correspondence: Jaime A. Teixeira da Silva, P. O. Box 7, Miki-cho post office, Ikenobe 3011-2, Kagawa-ken, 761-0799, Japan. email: jaimetex[at]yahoo.com Article received on the 30th January, 2015. Article accepted on the 05th May, 2015. Conflict of Interest: The author declares no conflicts of interest. Original Article KOME − An International Journal of Pure Communication Inquiry Volume 3 Issue 1, p. 81-87. © The Author(s) 2015 Reprints and Permission: kome@komejournal.com Published by the Hungarian Communication Studies Association Issues in science publishing: what’s hot and what’s not? Teixeira da Silva, J.A. 82 predatory journals, leaving scientists in a quagmire. This paper serves two purposes: to raise red flags and to call for greater awareness and discussion of these issues.

/pdf/issues-in-science-publishing-what-s-hot-and-what-s-not-4whrueupjk.pdf

Issues in Science Publishing. What's Hot and What's not?

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