Natural Genetic Engineering Research Articles

The mechanisms underpinning lateral gene transfer between grasses

Societal Impact StatementLateral gene transfer (LGT) refers to the transmission of genetic material without sexual reproduction. LGT is widespread in a number of plant species, including grasses. But how these genes of foreign origin got there is presently unknown. In this review, we show that transformation techniques used to genetically modify organisms could occur in the wild and be responsible for the frequently observed grass‐to‐grass LGTs. The distinction between natural evolutionary processes and genetic engineering might be arbitrary, and its validity will be further debated as agricultural biotechnology becomes more widely used and examples of “natural genetic engineering” through LGT increase.SummaryLateral gene transfer (LGT) is the transmission of genetic material among species without sexual reproduction. LGT was initially thought to be restricted to prokaryotes, but it has since been reported in a wide range of eukaryotes, including plants. Grasses seem to be particularly prone to LGT and frequently exchange genes among species. However, the mechanism(s) facilitating these transfers in this economically and ecologically important group of plants are debated. Here, we review vector‐mediated, direct tissue‐to‐tissue contact, wide‐crossing and reproductive contamination LGT mechanisms and discuss the likelihood of each in light of recent studies. Of particular relevance are transformation approaches that require minimal human intervention to transfer DNA among grasses in the lab that could mimic the mechanisms facilitating grass‐to‐grass LGT in the wild. These approaches include relatively simple techniques, such as pollen tube pathway‐mediated transformation, that take advantage of the permeability of the reproductive process to introduce alien genetic material from a third individual into an embryo. This process could be easily mirrored in the wild where pollen from one species lands on the stigma of another, acting as a source of alien DNA that can ultimately contaminate the reproductive process. This contamination is likely to be prevalent in wind pollinated species such as grasses, where the rates of illegitimate pollination will be high. In conclusion, plant transformation methods requiring minimal intervention are likely paralleled in the wild where they act as the mechanism underpinning LGT between distantly related grass species.

Editorial of International Journal of Pharmacy and Integrated Health Sciences

It is a great pleasure to introduce this issue on emerging ideas in health services research, biological, pharmaceutical, integrated health sciences in the International Journal of Pharmacy & Integrated Health Sciences (IJPIHS). We editor encourage studies with rigorous methodology and contributions because this is essential to ensure that the conclusions drawn from the journal's publications are true and reliable. All articles provide interesting, novel and useful results covering different areas pharmaceutical chemistry, pharmaceutics, pharmacogenomics, pharmacology, natural product research, nanotechnology, bioinformatics, biotechnology, environmental sciences and genetic engineering. The newest studies dealing with biomedical applications are summarized in this issue of IJPIHS, with "new frontiers" playing a crucial role in this regard. Review articles and original research covering all facets of pharmaceutical and integrated health sciences, as well as cutting-edge protocols and techniques to assess healthcare professionals' knowledge, attitudes, and practices regarding various clinical issues, are among the contributions for this issue.

Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane.

Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there is still much to be investigated regarding antisense transcripts in plants. A systematic review of scientific publications available in the Web of Science databases was conducted to contextualize how the studying of antisense transcripts has been addressed. Studies were classified considering three categories: “Natural antisense” (208), artificial antisense used in “Genetic Engineering” (797), or “Natural antisense and Genetic Engineering”-related publications (96). A similar string was used for a systematic search in the NCBI Gene database. Of the 1132 antisense sequences found for plants, only 0.8% were cited in PubMed and had antisense information confirmed. This value was the lowest when compared to fungi (2.9%), bacteria (2.3%), and mice (54.1%). Finally, we present an update for the cis-NATs identified in Saccharum spp. Of the 1413 antisense transcripts found in different experiments, 25 showed concordant expressions, 22 were discordant, 1264 did not correlate with the cognate genes, and 102 presented variable results depending on the experiment.

Genetic Approaches to Enhance Multiple Stress Tolerance in Maize.

The multiple-stress effects on plant physiology and gene expression are being intensively studied lately, primarily in model plants such as Arabidopsis, where the effects of six stressors have simultaneously been documented. In maize, double and triple stress responses are obtaining more attention, such as simultaneous drought and heat or heavy metal exposure, or drought in combination with insect and fungal infestation. To keep up with these challenges, maize natural variation and genetic engineering are exploited. On one hand, quantitative trait loci (QTL) associated with multiple-stress tolerance are being identified by molecular breeding and genome-wide association studies (GWAS), which then could be utilized for future breeding programs of more resilient maize varieties. On the other hand, transgenic approaches in maize have already resulted in the creation of many commercial double or triple stress resistant varieties, predominantly weed-tolerant/insect-resistant and, additionally, also drought-resistant varieties. It is expected that first generation gene-editing techniques, as well as recently developed base and prime editing applications, in combination with the routine haploid induction in maize, will pave the way to pyramiding more stress tolerant alleles in elite lines/varieties on time.

The evolution of evolutionary processes in organismal and cancer evolution

The evolution of early life and of contemporary viruses has been driven in significant part by random genetic mutations, while modern unicellular and organismal evolution primarily leverages evolved, efficient and active cell biology processes for adaptive changes prior to selection. Random mutations are often buffered by cell homeostasis, or they have a negative role, e.g., by causing death or monogenic diseases, or by triggering real-time cancer evolution. Accordingly, the Modern Synthesis theory no longer adequately describes the efficient, often punctuated and at times directionally adaptive natural genetic engineering (NGE) processes deduced from the DNA record of evolution.Similarly, the somatic mutation theory (SMT) of cancer describes driver mutations that can trigger oncogenesis, and passenger mutations characteristic of periods of genetic microevolution in cancer. At the precancerous stage, most somatic mutations are repaired or buffered in the cell, aberrant cells are removed, or organismal bioelectric tissue signals or other physiological functional networks maintain control of rogue, mutated cells. However, the SMT is not sufficient to describe the observed punctuated macroevolution of cancer-cell genes, chromosomes, karyotypes and epigenomes, nor of expressed cancer-cell transcriptomes, proteomes and epiproteomes, which include non-DNA-templated post-translational modifications, protein-protein interactions and metabolites. Moreover, punctuated cancer cell macroevolution often culminates in macro-effects, which include epithelial-mesenchymal transitions (EMT), cancer cell polyploidies and even giant multinucleated cancer cells that drive cancer progression, therapy resistance and metastasis. All of this cancer-cell evolution competes in a molecular and cellular arms race with host immune cells and antibodies, as well as with the host tumor microenvironment.Empirically observed punctuated, multilevel and multiclonal cancer macroevolution, and the concomitant, rapid co-development of the host immune system and tumor microenvironment, can occur with the efficiency, speed and lethality of cancer that is enabled by evolved, active natural genetic engineering (NGE) mechanisms. NGE affects both vertical cancer-cell genomic inheritance and evolution towards therapy resistance and metastasis, as well as viral or cancer-cell exosome vector-driven horizontal gene transfers that contributes to cancer cell cooperation, or to transforming previously non-cancerous somatic cells into destabilized cancer cells during metastasis.In addition, externally driven, irreversible and transferable (EDIT) adaptations are exemplified by mitotically heritable, non-templated cancer cell epigenetics, and by mitotically heritable cancer-cell surface protein and lipid glycosylation, as important examples of fast time-scale molecular evolution mechanisms in which genes are followers, similar to evo-devo processes in organismal evolution.

Bioinspired High-Degrees of Freedom Soft Robotic Glove for Restoring Versatile and Comfortable Manipulation.

The human hand is one of the most complex and compact grippers that has arisen as a product of natural genetic engineering; it is highly versatile, as it handles power and precision tasks. Since proper contact points and force directions are required to ensure versatility and secure a stable grip on an object, there must be a large workspace and controllable tip force directions for the digits. Although they are important, many individuals with neuromuscular diseases experience loss of these features. Thus, we propose a high-degree-of-freedom (DOF) soft robotic glove inspired by the anatomical features of human hands. The mechanism for adjusting the position and force direction of each tip is based on the structure of the extrinsic and intrinsic muscle-tendon units. The large thumb workspace was achieved by assisting opposition/reposition and flexion/extension to enable various grasping postures. A bidirectional actuation control mechanism with a cable-actuated agonist and an elastomer antagonist increased the assisted DOF and maintained compactness. The kinematic and kinetic performances of our device were evaluated by performing tests with eight stroke survivors. The thumb workspace increased by 43%, 207%, and 248% in the distal-proximal, dorsal-palmar, and radial-ulnar directions, respectively. The pinching shear force decreased by 54% and 45% for the nonthumb digits and thumb, respectively. These device-assisted improvements allowed objects to be stably grasped and manipulated in various postures. The novel device can assist individuals with impaired hand function to improve their grasping performance. Clinical Research Information Service (CRIS) Registration Number: KCT0004855.

What prevents mainstream evolutionists teaching the whole truth about how genomes evolve?

The common belief that the neo-Darwinian Modern Synthesis (MS) was buttressed by the discoveries of molecular biology is incorrect. On the contrary those discoveries have undermined the MS. This article discusses the many processes revealed by molecular studies and genome sequencing that contribute to evolution but nonetheless lie beyond the strict confines of the MS formulated in the 1940s. The core assumptions of the MS that molecular studies have discredited include the idea that DNA is intrinsically a faithful self-replicator, the one-way transfer of heritable information from nucleic acids to other cell molecules, the myth of “selfish DNA”, and the existence of an impenetrable Weismann Barrier separating somatic and germ line cells. Processes fundamental to modern evolutionary theory include symbiogenesis, biosphere interactions between distant taxa (including viruses), horizontal DNA transfers, natural genetic engineering, organismal stress responses that activate intrinsic genome change operators, and macroevolution by genome restructuring (distinct from the gradual accumulation of local microevolutionary changes in the MS). These 21st Century concepts treat the evolving genome as a highly formatted and integrated Read–Write (RW) database rather than a Read-Only Memory (ROM) collection of independent gene units that change by random copying errors. Most of the discoverers of these macroevolutionary processes have been ignored in mainstream textbooks and popularizations of evolutionary biology, as we document in some detail. Ironically, we show that the active view of evolution that emerges from genomics and molecular biology is much closer to the 19th century ideas of both Darwin and Lamarck. The capacity of cells to activate evolutionary genome change under stress can account for some of the most negative clinical results in oncology, especially the sudden appearance of treatment-resistant and more aggressive tumors following therapies intended to eradicate all cancer cells. Knowing that extreme stress can be a trigger for punctuated macroevolutionary change suggests that less lethal therapies may result in longer survival times.

NAD(P)H‐Dependent Enzymes for Reductive Amination: Active Site Description and Carbonyl‐Containing Compound Spectrum

AbstractThe biocatalytic asymmetric synthesis of amines from carbonyl compounds and amine precursors presents an important advance in sustainable synthetic chemistry. Oxidoreductases (ORs) that catalyze the NAD(P)H‐dependent reductive amination of carbonyl compounds directly to amines using amine donors present advantages complementary to those of amine transaminases (ATAs) with respect to selectivity, stability and substrate scope. Indeed some ORs accept alkyl and aryl amines as reaction partners enabling access to chiral secondary amine products that are not directly accessible using ATAs. Moreover, superior atom economy can usually be achieved as no sacrificial amines are required as with ATAs. In recent years a number of ORs that apparently catalyze both imine formation and imine reduction in the reductive amination of carbonyls has been identified using structure informed protein engineering, sequence analysis from natural biodiversity and increasingly a mixture of both. In this review we summarize the development of such enzymes from the engineering of amino acid dehydrogenases (AADHs) and opine dehydrogenases (OpDHs) to become amine dehydrogenases (AmDHs), which are active toward ketones devoid of any requisite carboxylate and/or amine functions, through to the discovery of native AmDHs and reductive aminases (RedAms), and the engineering of all of these scaffolds for improved or altered activity. Structural and mechanistic studies have revealed similarities, but also differences in the determinants of substrate binding and mechanism in the enzymes. The survey reveals that a complementary approach to enzyme discovery that utilizes both natural genetic resources and engineering can be combined to deliver biocatalysts that have significant potential for the industrial synthesis of chiral amines.magnified image

No genome is an island: toward a 21st century agenda for evolution.

Conventional 20th century evolution thinking was based on the idea of isolated genomes for each species. Any possibility of life-history inputs to the germ line was strictly excluded by Weismann's doctrine, and genome change was attributed to random copying errors. Today, we know that many life-history events lead to rapid and nonrandom evolutionary change mediated by specific cellular functions. There are many ways that genomes, viruses, cells, and organisms interact to generate evolutionary variation. These include cell mergers and activation of natural genetic engineering by stress, infection, and interspecific hybridization. In addition, we know molecular mechanisms for transmitting life-history information across generations through gametes. These discoveries require a new agenda for evolutionary theory and novel experimental designs to investigate the genomic impacts of stresses, biotic interactions, and sensory inputs coming from the environment. The review will offer some generic recommendations for enriching evolution experiments to incorporate new knowledge and find answers to previously excluded questions.

Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in Clostridium acetobutylicum ATCC 824.

Bacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into commodity chemicals by the anaerobic bacterium Clostridium acetobutylicum is a promising alternative source to fossil fuel-derived chemicals. Recently, it was demonstrated that xylose is not appreciably fermented in the presence of arabinose, revealing a hierarchy of pentose utilization in this organism (L. Aristilde, I. A. Lewis, J. O. Park, and J. D. Rabinowitz, Appl Environ Microbiol 81:1452-1462, 2015, https://doi.org/10.1128/AEM.03199-14). The goal of the current study is to characterize the transcriptional regulation that occurs and perhaps drives this pentose hierarchy. Carbohydrate consumption rates showed that arabinose, like glucose, actively represses xylose utilization in cultures fermenting xylose. Further, arabinose addition to xylose cultures led to increased acetate-to-butyrate ratios, which indicated a transition of pentose catabolism from the pentose phosphate pathway to the phosphoketolase pathway. Transcriptome sequencing (RNA-Seq) confirmed that arabinose addition to cells actively growing on xylose resulted in increased phosphoketolase (CA_C1343) mRNA levels, providing additional evidence that arabinose induces this metabolic switch. A significant overlap in differentially regulated genes after addition of arabinose or glucose suggested a common regulation mechanism. A putative open reading frame (ORF) encoding a potential catabolite repression phosphocarrier histidine protein (Crh) was identified that likely participates in the observed transcriptional regulation. These results substantiate the claim that arabinose is utilized preferentially over xylose in C. acetobutylicum and suggest that arabinose can activate carbon catabolite repression via Crh. Furthermore, they provide valuable insights into potential mechanisms for altering pentose utilization to modulate fermentation products for chemical production. IMPORTANCE Clostridium acetobutylicum can ferment a wide variety of carbohydrates to the commodity chemicals acetone, butanol, and ethanol. Recent advances in genetic engineering have expanded the chemical production repertoire of C. acetobutylicum using synthetic biology. Due to its natural properties and genetic engineering potential, this organism is a promising candidate for converting biomass-derived feedstocks containing carbohydrate mixtures to commodity chemicals via natural or engineered pathways. Understanding how this organism regulates its metabolism during growth on carbohydrate mixtures is imperative to enable control of synthetic gene circuits in order to optimize chemical production. The work presented here unveils a novel mechanism via transcriptional regulation by a predicted Crh that controls the hierarchy of carbohydrate utilization and is essential for guiding robust genetic engineering strategies for chemical production.

Microbiome Medicine: This Changes Everything

Microbiome Medicine: This Changes Everything

The Agrobacterium Phenotypic Plasticity (Plast) Genes.

The transfer of T-DNA sequences from Agrobacterium to plant cells is a well-understood process of natural genetic engineering. The expression of T-DNA genes in plants leads to tumors, hairy roots, or transgenic plants. The transformed cells multiply and synthesize small molecules, called opines, used by Agrobacteria for their growth. Several T-DNA genes stimulate or influence plant growth. Among these, iaaH and iaaM encode proteins involved in auxin synthesis, whereas ipt encodes a protein involved in cytokinin synthesis. Growth can also be induced or modified by other T-DNA genes, collectively called plast genes (for phenotypic plasticity). The plast genes are defined by their common ancestry and are mostly found on T-DNAs. They can influence plant growth in different ways, but the molecular basis of their morphogenetic activity remains largely unclear. Only some plast genes, such as 6b, rolB, rolC, and orf13, have been studied in detail. Plast genes have a significant potential for applied research and may be used to modify the growth of crop plants. In this review, I summarize the most important findings and models from 30years of plast gene research and propose some outlooks for the future.

Living Organisms Author Their Read-Write Genomes in Evolution.

Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with “non-coding” DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called “non-coding” RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

Biological action in Read-Write genome evolution.

Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with 'non-coding' DNA content rather than with protein-coding capacity in the genome. Coincidentally, 'non-coding' RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax

Sympatric speciation (SS), i.e., speciation within a freely breeding population or in contiguous populations, was first proposed by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection] and is still controversial despite theoretical support [Gavrilets S (2004) Fitness Landscapes and the Origin of Species (MPB-41)] and mounting empirical evidence. Speciation of subterranean mammals generally, including the genus Spalax, was considered hitherto allopatric, whereby new species arise primarily through geographic isolation. Here we show in Spalax a case of genome-wide divergence analysis in mammals, demonstrating that SS in continuous populations, with gene flow, encompasses multiple widespread genomic adaptive complexes, associated with the sharply divergent ecologies. The two abutting soil populations of S. galili in northern Israel habituate the ancestral Senonian chalk population and abutting derivative Plio-Pleistocene basalt population. Population divergence originated ∼0.2-0.4 Mya based on both nuclear and mitochondrial genome analyses. Population structure analysis displayed two distinctly divergent clusters of chalk and basalt populations. Natural selection has acted on 300+ genes across the genome, diverging Spalax chalk and basalt soil populations. Gene ontology enrichment analysis highlights strong but differential soil population adaptive complexes: in basalt, sensory perception, musculature, metabolism, and energetics, and in chalk, nutrition and neurogenetics are outstanding. Population differentiation of chemoreceptor genes suggests intersoil population's mate and habitat choice substantiating SS. Importantly, distinctions in protein degradation may also contribute to SS. Natural selection and natural genetic engineering [Shapiro JA (2011) Evolution: A View From the 21st Century] overrule gene flow, evolving divergent ecological adaptive complexes. Sharp ecological divergences abound in nature; therefore, SS appears to be an important mode of speciation as first envisaged by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection].

Stress-related hormones and glycinebetaine interplay in protection of photosynthesis under abiotic stress conditions.

Plants subjected to abiotic stresses such as extreme high and low temperatures, drought or salinity, often exhibit decreased vegetative growth and reduced reproductive capabilities. This is often associated with decreased photosynthesis via an increase in photoinhibition, and accompanied by rapid changes in endogenous levels of stress-related hormones such as abscisic acid (ABA), salicylic acid (SA) and ethylene. However, certain plant species and/or genotypes exhibit greater tolerance to abiotic stress because they are capable of accumulating endogenous levels of the zwitterionic osmolyte-glycinebetaine (GB). The accumulation of GB via natural production, exogenous application or genetic engineering, enhances plant osmoregulation and thus increases abiotic stress tolerance. The final steps of GB biosynthesis occur in chloroplasts where GB has been shown to play a key role in increasing the protection of soluble stromal and lumenal enzymes, lipids and proteins, of the photosynthetic apparatus. In addition, we suggest that the stress-induced GB biosynthesis pathway may well serve as an additional or alternative biochemical sink, one which consumes excess photosynthesis-generated electrons, thus protecting photosynthetic apparatus from overreduction. Glycinebetaine biosynthesis in chloroplasts is up-regulated by increases in endogenous ABA or SA levels. In this review, we propose and discuss a model describing the close interaction and synergistic physiological effects of GB and ABA in the process of cold acclimation of higher plants.

Physiology of the read-write genome.

Discoveries in cytogenetics, molecular biology, and genomics have revealed that genome change is an active cell-mediated physiological process. This is distinctly at variance with the pre-DNA assumption that genetic changes arise accidentally and sporadically. The discovery that DNA changes arise as the result of regulated cell biochemistry means that the genome is best modelled as a read-write (RW) data storage system rather than a read-only memory (ROM). The evidence behind this change in thinking and a consideration of some of its implications are the subjects of this article. Specific points include the following: cells protect themselves from accidental genome change with proofreading and DNA damage repair systems; localized point mutations result from the action of specialized trans-lesion mutator DNA polymerases; cells can join broken chromosomes and generate genome rearrangements by non-homologous end-joining (NHEJ) processes in specialized subnuclear repair centres; cells have a broad variety of natural genetic engineering (NGE) functions for transporting, diversifying and reorganizing DNA sequences in ways that generate many classes of genomic novelties; natural genetic engineering functions are regulated and subject to activation by a range of challenging life history events; cells can target the action of natural genetic engineering functions to particular genome locations by a range of well-established molecular interactions, including protein binding with regulatory factors and linkage to transcription; and genome changes in cancer can usefully be considered as consequences of the loss of homeostatic control over natural genetic engineering functions.

Evolution evolves: physiology returns to centre stage

Denis Noble, Eva Jablonka, Michael J. Joyner, Gerd B. Muller and Stig W. Omholt University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, UK Tel Aviv University, Cohn Institute for the History andPhilosophyof Science and Ideas, Ramat Aviv, Israel Mayo Clinic, Rochester, MN, USA University of Vienna, Department of Theoretical Biology, Vienna, Austria Norwegian University of Science and Technology, Faculty of Medicine, Trondheim, Norway

MANAGING CHILLING INJURY IN FRUITS

Most tropical and subtropical fruits are susceptible to chilling injury, mainly manifested as pitting, surface or internal browning, failure to ripening, development of a woolly or leathery texture, and decay. The development of these chilling injury symptoms negatively affects fruit quality and thus shortens storage life. Chilling injury of fruits can be alleviated by physical techniques such as low temperature conditioning, heat treatment, controlled or modified atmosphere storage, waxing, and UV-C irradiation, by chemical treatments with methyl jasmonate (MeJA), methyl salicylate (MeSA), γ-aminobutyric acid (GABA), 1-methylcyclopropene (1-MCP), nitric oxide, oxalic acid, or other natural compounds and genetic engineering. Treatment with MeJA enhances antioxidant activity, increases endogenous GABA and proline content and maintains a higher degree of unsaturation of membrane lipid in loquat fruit. GABA treatment enhances the accumulation of endogenous GABA and proline, induces higher antioxidant activity, and maintains higher adenosine triphosphate (ATP) content and energy charge in peaches. The combination of heat with MeJA or MeSA treatment has a synergistic effect on alleviating chilling injury and inducing higher antioxidant activity in peach fruit. For loquat, avocado, pineapple, and persimmon fruits whose chilling injury is enhanced by increased ethylene production, 1-MCP can be used to reduce its development. Low temperature conditioning activates the expression of membrane lipid modification enzymes such as fatty acid desaturase (FAD) and lipid transfer protein (LTP), whereas heat treatment induces the expression of various stress-related genes, including heat shock proteins (HSPs), dehydrin and universal stress protein (USP), increases antioxidant activity and maintains membrane stability in citrus fruits. Genetic engineering has the potential to enhance chilling tolerance by generation of genetically-modified fruits with overexpressed genes that encode HSPs and antioxidant enzymes.

Implications of the Read–Write Genome view

I am pleased to see that commentators from such disparate backgrounds (genomics, physiology, cancer research, evolutionary computation and physics) agree that there is benefit in rethinking the genome as a RW memory organelle under cell control [1]. This agreement indicates that the RW Genome will prove fruitful and adaptable to many areas of the life sciences and possibly even to the hard and information sciences as well. There are also dissenting interpretations. Let us deal with the dissents first and then move on to further implications of the RW Genome view. While grudgingly acknowledging at the end of his comment that “genomes are indeed read–write”, molecular geneticist Damon Lisch repeats quite a few of the standard (and easily rebutted) objections to the idea that cells actively engage natural genetic engineering (NGE) for useful genome inscriptions to cope with episodes of evolutionary challenge [2]. This is surprising, coming from the author of a paper on the action of maize transposons in “directional modification of genes through biased insertion and DNA acquisition” [3]. A single example will illustrate the limitations of Lisch’s reservations. He characterizes mobile genetic elements (MGEs) as “selfish” “parasitic entities” and states, “it is extremely unlikely that any but a tiny fraction of the insertions contribute to meaningful differences in the morphology of related species”. What Lisch considered “extremely unlikely” is now established genome science. He failed to notice that I indicated where we do have minimum quantitative estimates of the contributions of MGEs to functionally usefully genome elements in mammals. Last year, these stood at 280 000, or 19.1% of all conserved (i.e., positively selected) differences between eutherian mammals and marsupials [4]. Moreover, MGEs have been identified as contributing to between 11 and 20% of human regulatory elements [5]. In a similar dubious vein, Maxim Frank-Kamenetskii argues that the examples of genome RW character do not invalidate the “universal” principles of conventional views about genomic information [6]. I have to disagree strongly on two grounds. In my understanding of the last 60 years of molecular biology, the data show that genome inscriptions are the rule, not the exception. Empirically, the evidence of genome inscriptions needed for progress through the cell cycle, multicellular development, and evolutionary innovation overwhelms any claim that they are exceptional, rather than fundamental, events. From an epistemological perspective, I further find it impossible to accept “universals” where there are well-documented counter-examples [7]. Our job as scientists is to formulate our theories to incorporate