Plant Phenomics: Fundamental Bases,Software and Hardware Platforms,and Machine Learning

Russian Journal of Plant Physiology - In recent years, a new branch of plant physiology, plant phenomics, which focuses on identifying patterns of organization and changes in plant Phenomes, i.e.,...     

Phylogenetics and seed morphology of African Nymphoides (Menyanthaceae)

We evaluated the boundaries among Nymphoides (Menyanthaceae) species in Africa, a region where the genus has received relatively little attention. We gathered morphological data from seeds using light and scanning electron microscopy, and we conducted molecular phylogenetic analyses using nuclear sequence data from the internal transcribed spacer (ITS) region. Morphological and molecular features distinguished six species and affirmed their respective geographic ranges. No African specimens were attributable to Nymphoides indica, even though this paleotropical species previously had been understood to grow in Africa. We establish the new combination Nymphoides senegalensis (G. Don) Tippery, based on an established African basionym, to accommodate the specimens formerly identified as N. indica. Phylogenetic analyses resolved two distinct clades containing African species. The majority of African species are closely related to neotropical species, with which they share similar petal ornamentation. The morphologically distinct N. ezannoi shares floral and phylogenetic similarity with species from North America and Asia. Results presented here support prior hypotheses that allopolyploid species in the Americas may have originated from one or more parental lineages in Africa. Seed morphological characters remain some of the most reliable features for identifying species, particularly for herbarium specimens lacking observable floral characters.     

Intensive protein synthesis in neurons and phosphorylation of beta-amyloid precursor protein and tau-protein are triggering factors of neuronal amyloidosis and Alzheimer’s disease

Studies of Alzheimer’s disease have become particularly important and attract now much attention of scientists all over the world due to worldwide dissemination of this dangerous disorder. Causes of this pathology still remain unknown, while the final image, originally obtained on microscopic brain sections from patients with this disease more than a hundred years ago, is well familiar to clinicians. This includes deposition of amyloid-β (Aβ) in the brain tissue of senile plaques and fibrils. Many authors believe that the deposition of Aβ provokes secondary neuronal changes, responsible for death of neurons. Other authors associate the death of neurons with hyperphosphorylation of tau-proteins, which form neurofibrillar tangles inside nerve cells and cause their death. Creation of methods of preclinical diagnostics and effective treatment of Alzheimer’s disease requires novel knowledge: on the nature of triggering factors of sporadic forms of Alzheimer’s disease, on cause-effect relationships of phosphorylation of amyloid precursor protein with formation of pathogenic beta-amyloids, on the relationship between these factors underlying tau-protein hyperphosphorylation and neuron death. In this review we have analyzed reports describing increased intensity of protein synthesis in neurons under normal and various stress conditions, possibility of development of energy imbalance of neurons and activation of their protective systems. Phosphorylation and hyperphosphorylation of tau-proteins is also tightly associated with protective mechanisms of cells and with processes of evacuation of phosphates, adenosine monophosphates and pyrophosphates from the region of protein synthesis. Prolonged highly intensive protein synthesis causes overload of protective mechanisms and impairments in concerted metabolic processes. This leads to neuronal dysfunction, transport collapse, and death of neurons.     

Role of heparin in the formation of food lipemia

Influence of endogenic and exogenic heparin in vivo on the basic forms of serum lipids content: cholesterol ethers, triacylglycerols, free fatty acids; as well as that glycosaminoglycan effect in vivo and in vitro on total lipoproteine lipase (LPL) activity and lecithin-cholesterol acyltransferase (LCAT) activity of human blood serum were investigated on food lipidemia model. The decrease of intercell reserve heparin content and increase of the background and post-heparin levels of blood serum LPL activity were indicated after two hours food load. The role of two factors, endogenic heparin being one of them, in the increase of postprandial LPL activity of blood serum were discussed. At the same time, some inhibition of blood serum LCAT activity two hours after food reception (evidently, as a result of endogenic heparin action) and to a considerable extent inhibition of cholesterol etherification under the action of exogenic heparin in vivo were ascertain. Heparin in vitro (50 U/ml of blood serum) did not influence LCAT and total LPL activities. It was summarised that endogenic heparin is a factor, taking part in lipolysis processes regulation.     

The Effect of Cu2+ on Ion Transport Systems of the Plant Cell Plasmalemma

Changes in plasmalemma permeability caused by excessive Cu2+ levels were examined in cells of a freshwater alga (Nitella flexilis) using a conventional microelectrode voltage-clamp technique. A rapid Cu2+-induced increase of plasmalemma conductance starting from 5 [mu]M Cu2+ was shown. Cu2+-induced plasmalemma conductance (ClGm) was nonselective and potential-independent, resembling the conductance of nonselective ionic leakage of the plasmalemma. The K+ channel conductance was shown to be unaltered by Cu2+, and a decrease in plasmalemma Cl- channel conductance at Cu2+ concentrations above 5 [mu]M was found. The depression of Cl- channels and ClGm were time-, dosage-, and Ca2+-dependent processes, revealing a great similarity in all parameters, with Ca2+ causing the preventive effect by shifting the effective Cu2+ concentrations to higher levels. This phenomenon may be explained by the same Cu2+-modified target on the plasmalemma both for ClGm and Cl- channel depression. In addition, a reversible, inhibitory effect of Cu2+ (>10 [mu]M) on the light-stimulated H+-ATPase electrogenic pump in the plasmalemma was demonstrated. This effect was Ca2+- independent, which made it possible to distinguish it from ClGm. Therefore, the Cu2+-induced dramatic alterations in plant cell plasmalemma permeability are caused mainly by nonselective conductance increases and electrogenic pump inhibition.     

Engineered silver nanoparticles are sensed at the plasma membrane and dramatically modify the physiology of Arabidopsis thaliana plants

Silver nanoparticles (Ag NPs) are the world's most important nanomaterial and nanotoxicant. The aim of this study was to determine the early stages of interactions between Ag NPs and plant cells, and to investigate their physiological roles. We have shown that the addition of Ag NPs to cultivation medium, at levels above 300 mg L^?1, inhibited Arabidopsis thaliana root elongation and leaf expansion. This also resulted in decreased photosynthetic efficiency and the extreme accumulation of Ag in tissues. Acute application of Ag NPs induced a transient elevation of [Ca²⁺]_cyt and the accumulation of reactive oxygen species (ROS; partially generated by NADPH oxidase). Whole‐cell patch‐clamp measurements on root cell protoplasts demonstrated that Ag NPs slightly inhibited plasma membrane K⁺ efflux and Ca²⁺ influx currents, or caused membrane breakdown; however, in excised outside‐out patches, Ag NPs activated Gd³⁺‐sensitive Ca²⁺ influx channels with unitary conductance of approximately 56 pS. Bulk particles did not modify the plasma membrane currents. Tests with electron paramagnetic resonance spectroscopy showed that Ag NPs were not able to catalyse hydroxyl radical generation, but that they directly oxidized the major plant antioxidant, l ‐ascorbic acid. Overall, the data presented shed light on mechanisms of the impact of nanosilver on plant cells, and show that these include the induction of classical stress signalling reactions (mediated by [Ca²⁺]_cyt and ROS) and a specific effect on the plasma membrane conductance and the reduced ascorbate.     

Prediction of the three-dimensional structure of aflatoxin of Aspergillus flavus by homology modelling

Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus spp. The toxic effects of aflatoxins have adverse consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a protein containing a zinc-finger DNA-binding motif. AFLR-Protein three-dimensional model was generated using Robetta server. The modeled AFLR-Protein was further optimization and validation using Rampage. In the simulations, we monitored the backbone atoms and the C-α-helix of the modeled protein. The low RMSD and the simulation time indicate that, as expected, the 3D structural model of AFLR-protein represents a stable folding conformation. This study paves the way for generating computer molecular models for proteins whose crystal structures are not available and which would aid in detailed molecular mechanism of inhibition of aflatoxin.     

Lipoprotein metabolism in patients with diabetes of type II

Changes in contents of blood serum lipoproteins (LP) and activity of enzymes of their transformation were investigated in patients with diabetes mellitus of type II. It was found out that mechanisms of increasing of apoB-containing LP in these patients were on the one hand in enhancing of the processes of their new-formation in the liver. On the other hand, retardation of their arrival to peripheral tissues might be observed, that as a whole resulted in continuous LPLD circulation in blood. Above-mentioned processes were associated with a reciprocal decreasing of the amount of all the apoA-containing LP fractions examined. To a certain extent mechanisms of disturbance of LP metabolism in the circulation bed were stipulated by changes of function of the enzyme catalyzing their transformation.