Abir U Igamberdiev

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Verified

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• Ph.D., D.Sc.
• Professor (Full) at Memorial University of Newfoundland

Rubisco is the most abundant protein on Earth that serves as the primary engine of carbon assimilation. It is characterized by a slow rate and low specificity for CO2 leading to photorespiration. We analyze here the challenges of operation of this enzyme as the main carbon fixation engine. The high concentration of Rubisco exceeds that of its subst...

Under hypoxic conditions, plant mitochondria preserve the capacity to oxidize external NADH, NADPH and tricarboxylic acid cycle substrates. Nitrite serves as an alternative electron acceptor at the level of cytochrome oxidase, with possibly complex III and the alternative oxidase also being involved. Nitric oxide is a significant product of the rea...

The computational process is based on the activity linking mathematical equations to a materialized physical world. It consumes energy which lower limit is defined by the set of Planck's values, i.e. by the physical structure of the Universe. We discuss computability from the quantum measurement framework. Effective quantum computation is possible...

The “superfruit” lingonberry (Vaccinium vitis-idaea L.) is well known for its enormous health benefits and rich phytochemical contents. However, its regeneration and propagation face significant challenges due to the woody nature of the plant and poor proliferation rates using conventional methods. By using juvenile leaf explants of two V. vitis-id...

Hyperhydricity is a significant challenge in the tissue culture of blueberry plantlets, affecting their propagation, survival and quality, which results in economic losses for industrial blueberry micropropagation. The in vitro liquid propagation of two half-highbush blueberry hybrids, HB1 and HB2, showed that a Growtek stationary bioreactor cultur...

Vaccinium membranaceum (black huckleberry) is known for its high content of bioactive compounds. This study introduces a novel approach for bioreactor micropropagation using stationary (Growtek) and temporary immersion (RITA) bioreactor systems using a liquid nutrient medium to enhance the in vitro propagation of black huckleberry. Adventitious sho...

Alternative oxidase (AOX) regulates the level of reactive oxygen species and nitric oxide (NO) in plants. While under normoxic conditions it alleviates NO formation, there are several indications that in the conditions of low oxygen such as during seed germination before radicle protrusion, in meristematic stem cells, and in flooded roots AOX can b...

Different types of microRNA participate in the post-transcriptional regulation of target genes. The content of several hypoxia-dependent miRNAs in plant cells, including miR775, increases in the conditions of oxygen deficiency. Electrophoretic studies of total RNA samples from the leaves of flooded seedlings of maize (Zea mays L.) revealed the pres...

Nucleoside mono-, di- and triphosphates (NMP, NDP, and NTP) and their deoxy- counterparts (dNMP, dNDP, dNTP) are involved in energy metabolism and are the building blocks of RNA and DNA, respectively. The production of NTP and dNTP is carried out by several NMP kinases (NMPK) and NDP kinases (NDPK). All NMPKs are fully reversible and use defined Mg...

Dietary intake of Vaccinium berries has demonstrated significant potential in preventing many risk factors associated with metabolic syndromes in the human population. In recent years, a multitude of research has shown the role of antioxidants derived from Vaccinium berries on chronic diseases such as cardiovascular disorders, diabetes, obesity, an...

Significance: Seed germination and seedling establishment are characterized by changes in the intracellular redox state modulated by accelerated production of nitric oxide (NO) and reactive oxygen species (ROS). Redox regulation and enhanced accumulation of NO and ROS, approaching excessively high levels during seed imbibition, are critically impor...

Glutamate is an essential amino acid in both the energy and biosynthetic processes in plant cells. The aim of this work was to study changes in glutamate metabolism upon irradiation of maize (Zea mays L.) leaves with light of different spectral compositions, as well as to identify mechanisms regulating the work of enzymes involved in the studied pr...

The effect of salt stress (150 mM NaCl) on the expression of genes, methylation of their promoters, and enzymatic activity of glutamate dehydrogenase (GDH), glutamate decarboxylase (GAD), and the 2-oxoglutarate (2-OG)–dehydrogenase (2-OGDH) complex was studied in maize (Zea mays L.). GDH activity increased continuously under salt stress, being 3-fo...

The involvement of the microRNA miR165a in the light-dependent mechanisms of regulation of target genes in maize (Zea mays) has been studied. The light-induced change in the content of free miR165a was associated with its binding by the AGO10 protein and not with a change in the rate of its synthesis from the precursor. The use of knockout Arabidop...

Plant glycerate kinase (GK) was previously considered an exclusively chloroplastic enzyme of the glycolate pathway (photorespiration), and its sole predicted role was to return most of the glycolate-derived carbon (as glycerate) to the Calvin cycle. However, recent discovery of cytosolic GK revealed metabolic links for glycerate to other processes....

Nitrogen (N) is an essential nutrient for plants, and the sources from which it is obtained can differently affect their entire development as well as stress responses. Distinct inorganic N sources (nitrate and ammonium) can lead to fluctuations in the nitric oxide (NO) levels and thus interfere with nitric oxide (NO)-mediated responses. These coul...

Classical thermodynamics employs the state of thermodynamic equilibrium, characterized by maximal disorder of the constituent particles, as the reference frame from which the Second Law is formulated and the definition of entropy is derived. Non-equilibrium thermodynamics analyzes the fluxes of matter and energy that are generated in the course of...

In vitro propagation is an advanced vegetative propagation technology employed to produce a large number of high-quality plants in a limited time and space. Year- round production of relatively uniform disease and pest-free plants could be obtained using in vitro technologies. With the increasing demand for micropropagated plants, different micropr...

A key feature in the establishment of symbiosis between plants and microbes is the maintenance of the balance between the production of the small redox-related molecule, nitric oxide (NO) and its cognate scavenging pathways. During the establishment of symbiosis, a transition from a normoxic to a microoxic environment often takes place triggering t...

Main conclusion The preservation of quiescent center stem cell integrity in hypoxic roots by phytoglobins is exercised through their ability to scavenge nitric oxide and attenuate its effects on auxin transport and cell degradation. Under low oxygen stress, the retention or induction of phytoglobin expression maintains cell viability while loss or...

A proficient plant propagation technique using somatic embryogenesis was successfully established in lingonberry (Vaccinium vitis-idaea L.), a small evergreen shrub. The formation of callus and somatic embryos was observed in two lingonberry genotypes during the process. The most favorable conditions for embryogenic callus induction were observed o...

A unique exploration of teleonomy—also known as “evolved purposiveness”—as a major influence in evolution by a broad range of specialists in biology and the philosophy of science. The evolved purposiveness of living systems, termed “teleonomy” by chronobiologist Colin Pittendrigh, has been both a major outcome and causal factor in the history of li...

Lingonberry (Vaccinium vitis-idaea L.) is an important and valuable horticultural crop due to its high antioxidant properties. Plant tissue culture is an advanced propagation system employed in horticultural crops. However, the progeny derived using this technique may not be true-to-type. In order to obtain the maximum return of any agricultural en...

The code paradigm in biological and social sciences arises to Aristotle. For conscious activity, Aristotle introduced the notion of reflexive self-awareness in sense perception. This reflexive process generates the codes that signify sensual perceptive events and constrain human behavior. Coding systems grow via the generation of hypertextual state...

The expression and methylation of promoters of the genes encoding succinate dehydrogenase, fumarase, and NAD-malate dehydrogenase in maize (Zea mays L.) leaves depending on the light regime were studied. The genes encoding the catalytic subunits of succinate dehydrogenase showed suppression of expression upon irradiation by red light, which was abo...

Root growth in maize (Zea mays L.) is regulated by the activity of the quiescent center (QC) stem cells located within the root apical meristem. Here, we show that despite being highly hypoxic under normal oxygen tension, QC stem cells are vulnerable to hypoxic stress, which causes their degradation with subsequent inhibition of root growth. Under...

Oxygen deprivation by waterlogging reduces the productivity of several crop species, including the oil-producing crop Brassica napus L., which is highly sensitive to excess moisture. Among factors induced by oxygen deficiency are phytoglobins (Pgbs), heme-containing proteins known to ameliorate the response of plants to the stress. This study exami...

More than 15,000 scientific articles published since the late 1950s related to RNS action or detection in various plant materials are listed in the Web of Science database [...]

Oxygen deprivation (hypoxia) in the root due to waterlogging causes profound metabolic changes in the aerial organs depressing growth and limiting plant productivity in barley (Hordeum vulgare L.). Genome-wide analyses in waterlogged wild type (WT) barley (cv. Golden Promise) plants and plants over-expressing the phytoglobin 1 HvPgb1 [HvPgb1(OE)] w...

General structure of metabolism includes the reproduction of catalysts that govern metabolism. In this structure, the system becomes autopoietic in the sense of Maturana and Varela, and it is closed to efficient causation as defined by Robert Rosen. The autopoietic maintenance and operation of the catalysts takes place via the set of free nucleotid...

Free magnesium (Mg2+) represents a powerful signal arising from interconversions of adenylates (ATP, ADP and AMP). This is a consequence of the involvement of adenylate kinase (AK) which equilibrates adenylates and uses defined species of Mg-complexed and Mg-free adenylates in both directions of its reaction. However, cells contain also other rever...

Micropropagation is an advanced vegetative propagation technology used to produce a large number of high-quality plants in limited time and space and has been used extensively in Vaccinium species. Lingonberry (Vaccinium vitis-idaea L.) is a health-promoting fruit crop containing a high number of antioxidant properties. Different types of medium an...

The effect of salt stress on the expression of genes, the methylation of their promoters, and the enzymatic activity of succinate dehydrogenase (SDH) and succinic semialdehyde dehydrogenase (SSADH) was investigated in maize (Zea mays L.). The incubation of maize seedlings in a 150 mM NaCl solution for 24 h led to a several-fold increase in the acti...

In photosynthetic tissues in the light, the function of energy production is associated primarily with chloroplasts, while mitochondrial metabolism adjusts to balance ATP supply, regulate the reduction level of pyridine nucleotides, and optimize major metabolic fluxes. The tricarboxylic acid cycle in the light transforms into a non-cyclic open stru...

Limited methyl-specific restriction of genomic DNA by endonuclease MAL1 revealed the changes in its methyl status caused by adenine modification in maize (Zea mays L.) leaves under different light conditions (dark, light, irradiation by red and far-red light). Incubation in the light and irradiation by red light exhibited an activating effect on DN...

The goal-directedness of biological evolution is realized via the anticipatory achievement of the final state of the system that corresponds to the condition of its perfection in self-maintenance and in adaptability. In the course of individual development, a biological system maximizes its power via synergistic effects and becomes able to perform...

Until the middle of the 20th century, embryogenesis patterns were considered as based on a rigid, unidirectional ontogenetic development, whose nuclear programming yields an irreversibility feature for cellular determination. Further empirical pieces of evidence have provided new insights about a certain reversibility to cellular determination, fin...

Epigenetic variation plays a role in developmental gene regulation and responses to the environment. An efficient interaction of zeatin-induced cytosine methylation and secondary compounds has been displayed for the first time in tissue-culture shoots/plants of lingonberry (Vaccinium vitis-idaea L.) cultivar Erntedank in vitro (NC1, in a liquid med...

In plants, cortical microtubules and their associated proteins play crucial roles in fundamental cellular processes and responses to environmental stimuli. Here, we determined that the microtubule-associated protein CLASP (Cytoplasmic Linker Associated Protein) plays an important role in mitigating salt stress in Arabidopsis thaliana (Col-0). Armed...

The transgenic tobacco (Nicotiana tabacum L.) plants with the modified levels of alternative oxidase (AOX) were used to evaluate the physiological roles of AOX in regulating nitro-oxidative stress and metabolic changes after exposing plants to hypoxia for 6 h. Under normoxia, AOX expression resulted in the decrease of nitric oxide (NO) levels and o...

The transcript levels of the phytoglobin (Pgb) genes Pgb1 and Pgb3, and the protein content of Pgb1 were responsive to anaerobiosis in several tissues of barley (Hordeum vulgare L.). Oxygen deficiency induced the level of both Pgb transcripts and protein in aleurone layers and coleoptiles, as well as up-regulated both Pgb1 and Pgb3 in leaves, apexe...

Pesticides can seriously affect the respiratory chain of the mitochondria of many crops, reducing the intensity of plant growth and its yield. Studying the effect of pesticides on the bioenergetic parameters of intact plant mitochondria is a promising approach for assessing their toxicity. In this study, we investigated the effect of some pesticide...

Efim A. Liberman (1925–2011) can be considered as a founder of the new field of science that explores Natural Computation and its limits. He named it Chaimatics and suggested its generalization to the ultimate all-encompassing theory that unites biology, physics and mathematics. He made a number of experimental discoveries, including color coding i...

The plant mitochondrial electron transport chain influences carbon and nitrogen metabolism under near anoxic conditions through its involvement in the phytoglobin-nitric oxide cycle, where the respiratory chain reduces nitrite to nitric oxide (NO), followed by NO conversion to nitrate by class 1 phytoglobin. Wild type (WT) and transgenic tobacco (N...

Exposing plants to gradually increasing stress and to abiotic shock represents two different phenomena. The knowledge on plants’ responses following gradually increasing stress is limited, as many of the studies are focused on abiotic shock responses. We aimed to investigate how cowpea (Vigna unguiculata (L.) Walp.) plants respond to three common a...

Rice (Oryza sativa L.) and barley (Hordeum vulgare L.) are the cereal species differing in tolerance to oxygen deficiency. To understand metabolic differences determining the sensitivity to low oxygen, we germinated rice and barley seeds and studied changes in the levels of reactive oxygen species (ROS) and reactive nitrogen species (RNS), activiti...

Epigenetic variation plays a role in developmental gene regulation and responses to the environment. An efficient interaction of zeatin induced cytosine methylation and secondary compounds has been displayed for the first time in tissue-culture shoots of lingonberry ( Vaccinium vitis-idaea ) in vitro, in vivo and its cutting-cultivar Erntedank. Thr...

The contribution of Étienne Geoffroy Saint-Hilaire (1772–1844) to evolutionary biology is reviewed in commemoration of his 250th birthday. Geoffroy's views on saltational changes during embryogenesis of animals characterize him as a predecessor of the epigenetic concept of evolution, which is now developing in the frames of the extended evolutionar...

Valery Taliev (1872–1932) was one of the first natural scientists who investigated the importance of anthropogenic factors in the evolution and geographic distribution of higher plants. He outlined major parameters of the origin and spreading of weed plants, of the flora of riverbanks, and proposed a direct role of man in changing the balance betwe...

Vaccinium (L.) berry crops including blueberries, lingonberries, cranberries and huckleberries are native to the North of Canada. These healthy fruit crops with their high antioxidant, anti-inflammatory, antiulcer and antitumor activities play significant role for sustainable northern agriculture and/or for the Indigenous population of Canada. In v...

Blueberry (Vaccinium spp. L.) plants exhibit high potential of regeneration via adventitious shoot formation on a semi-solid medium followed by shoot elongation in a liquid medium under bioreactor systems. To find out whether DNA methylation plays a role during shoot elongation, we compared DNA methylation level in the regenerants of two in vitro-g...

Dihydroxyacid dehydratase (EC 4.2.1.9) participates in metabolism of branched chain amino acids, in CoA biosynthesis and in the conversion of hydroxycitric acid that accumulates in several plants. In maize (Zea mays L.), this enzyme is encoded by the two genes (Dhad1 and Dhad2), having different patterns of their expression during germination. We h...

The influence of salt stress on gene expression, promoter methylation, and enzymatic activity of the mitochondrial and cytosolic forms of aconitase and fumarase has been investigated in maize (Zea mays L.) seedlings. The incubation of maize seedlings in 150-mM NaCl solution resulted in a several-fold increase of the mitochondrial activities of acon...

The phenomenon of evolutionary complexification corresponds to the generation of new coding systems (defined as а codepoiesis by Marcello Barbieri). The whole process of generating novel coding statements that substantiate organizational complexification leads to an expansion of the system that incorporates externality to support newly generated co...

In the conditions of [Mg2+] elevation that occur, in particular, under low oxygen stress and are the consequence of the decrease of [ATP] and increase of [ADP] and [AMP], pyrophosphate (PPi) can function as an alternative energy currency in plant cells. In addition to its production by various metabolic pathways, PPi can be synthesized in the combi...

Mathematics is a powerful tool to express the computable part of the reality of the physical world. For living systems, mathematical relations emerge internally as an abstracting capacity in the course of development and adaptation to the external world. All living systems possess internal coding structures which represent their embedded descriptio...

Free magnesium (Mg²⁺) is a signal of the adenylate (ATP+ADP+AMP) status in the cells. It results from the equilibrium of adenylate kinase (AK), which uses Mg-chelated and Mg-free adenylates as substrates in both directions of its reaction. The AK-mediated primary control of intracellular [Mg²⁺] is finely interwoven with the operation of membrane-bo...

In this paper, we aim to unravel the structure of formal logic in relation to its emergence as a universal tool for understanding and description of reality. There are some extended variations of logic that treat time and/or space (e.g. temporal logic), however in general, formal logic is regarded as universal. This universality makes formal logic...

Plant tissue culture techniques have been extensively employed in commercial micropropagation to provide year-round production. Tissue culture regenerants are not always genotypically and phenotypically similar. Due to the changes in the tissue culture microenvironment, plant cells are exposed to additional stress which induces genetic and epigenet...

We analyze evolutionary views of Boris Kozo-Polyansky (1890–1957) who was the first who formulated the symbiotic theory of evolution as a concept in his book, Symbiogenesis: A New Principle of Evolution (1924). Later, starting from 1967, Lynn Margulis independently formulated and further developed the concept of symbiogenesis. Although the ideas on...

In this chapter, we bring together the essential insights of Chap. 9 on semantics and new concepts and units of meaning, Chap. 10 which analyzes different branches of philosophy, and Chaps. 11 and 12 on information and communication and their philosophy. This chapter is accordingly our first attempt at a new synthesis under the heading of a natural...

We compare concepts of change in Western science and philosophy and the Chinese classics in relation to views of the nature of reality and the forms of human thought. The classic Chinese I Ching or Book of Changes has been used for purposes of divination, but we argue that its major function has always been to provide insight into the underlying re...

All living systems possess the internal coding structures which represent their embedded description. They are anticipatory in the sense that the embedded description generates a deterministic model of their behavior. If the model does not provide a correct result, they can evolve due to acquisition of new statements inside the embedded description...

In this book, with its emphasis on Natural Philosophy, we have looked at a philosophy embedded in a realistic view of nature, co-existing with scientific perspectives in a dialectic relation. In recent major developments in the sciences and their philosophy, systems approaches are now widely used to try to identify some common, if possible simplify...

In this Chapter, we bring together our prior approaches to philosophy and logic, their application in science and their implications of these for systems theory. The previous Chap. 20 focused on the cognitive processes of individual humans in relation to society. These two threads come together here in a synthesis centered on the structure of and c...

This chapter analyzes the sub-field of anti-philosophy as a real component of any current picture of Philosophy in Reality. Despite its relatively limited scope in terms of volume of literature, authors in this field call attention to significant issues involving the nature of philosophy in relation to other domains of thought. The interesting vari...

With the additional background on the operation of Logic in Reality in hand, we will apply it to some specific additional familiar categories of change. Brenner demonstrated in 2017 that the principles of the Lupasco logic recapture something of the unity of knowledge present in classical Western thought and provide a bridge to a new picture of kno...

If a philosophical statement means something at all, has or conveys meaning, this fact does not and cannot stand in isolation. The meaning in question is not a solely epistemological concept, but puts natural philosophy in a dynamic relation with a dialectics and a logic. In this ‘meaning in motion’, we move from semantics to dynamics where meaning...

In the middle of the twentieth Century, the Franco-Romanian thinker Stéphane Lupasco proposed a unique, non-propositional and thus non-truth functional logic applicable to changes in real processes and systems. It was developed by Basarab Nicolescuas a logic of the included third term and further by one of us (Brenner) as a logic of and in reality....

This chapter develops the LIR notion of meaning as central not only to language and its semiotic structure but to existence. We contrast our approach to the logical philosophy of Peirce, which continues to set the standard for thinking in this area, introducing an alternative picture of semiotics and semiosis. The location of meaning in all entitie...

The domain of philosophy-as-such, philosophy as a separate discipline is directed toward the study of general principles. Examples are the unity of knowledge and speculative, ‘fundamental’ questions such as “why is there something rather than nothing?” The emphasis in this book has been on the philosophical implications of science, real process and...

This chapter is an attempt to make up for the absence of discussion in the literature of the implications of Lupasco’s logic and dialectics for philosophy as such. We show that despite the apparent disjunction between the ideas of Kant and Lupasco, a few points of conjunction can be found which, if anything, strengthen some of the former’s basic in...

Major parallels are suggested between the evolution of a chemical reaction from reactants to products and that of the semantic processes that are the usual subjects of philosophy and logic. We show that the key principles of chemistry—the activation energy and the transition state in chemical reactions—are applicable in more complex form to all ene...

Physics as science appeared when the frame of reference of external reality in relation to observer was formulated. This frame was first introduced by Galileo and became the basis of Newtonian mechanics. It thus was a basis for placing the fundamental concepts of time and space on a scientific basis. Later, the relation of the observer to external...

The origin of social systems lies in the emergence of the structure of the human subject who can incorporate an internal image of the external world. This structure, established on the basis of the dynamic referral of the conscious subject (self) to its symbolic image, acquires the potential to rationally describe the external world through the sem...

The major themes of the book are summarized: the search for a new synthesis of science and philosophy covering all aspects of real change; application of our logic and dialectics in the areas of communication, information and meaning; application of our logical-philosophical approach to the standard domains of philosophy; the emerging new role for...

Mathematics appeared in antiquity as a powerful tool to express the computability of reality. As an independent field of knowledge, it was founded in the West by Pythagoras. Plato, following Pythagoras, claimed the reality of mathematics as the true reality of the intelligible world as opposed to the false reality of the perceived world. This point...