A Principal Components Analysis and Functional Annotation of Differentially Expressed Genes in Brain Regions of Gray Rats Selected for Tame or Aggressive Behavior.

The process of domestication, despite its short duration as it compared with the time scale of the natural evolutionary process, has caused rapid and substantial changes in the phenotype of domestic animal species. Nonetheless, the genetic mechanisms underlying these changes remain poorly understood. The present study deals with an analysis of the transcriptomes from four brain regions of gray rats (Rattus norvegicus), serving as an experimental model object of domestication. We compared gene expression profiles in the hypothalamus, hippocampus, periaqueductal gray matter, and the midbrain tegmental region between tame domesticated and aggressive gray rats and revealed subdivisions of differentially expressed genes by principal components analysis that explain the main part of differentially gene expression variance. Functional analysis (in the DAVID (Database for Annotation, Visualization and Integrated Discovery) Bioinformatics Resources database) of the differentially expressed genes allowed us to identify and describe the key biological processes that can participate in the formation of the different behavioral patterns seen in the two groups of gray rats. Using the STRING- DB (search tool for recurring instances of neighboring genes) web service, we built a gene association network. The genes engaged in broad network interactions have been identified. Our study offers data on the genes whose expression levels change in response to artificial selection for behavior during animal domestication.

AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L.

The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions.

Candidate SNP Markers Significantly Altering the Affinity of TATA-Binding Protein for the Promoters of Human Hub Genes for Atherogenesis, Atherosclerosis and Atheroprotection.

Atherosclerosis is a systemic disease in which focal lesions in arteries promote the build-up of lipoproteins and cholesterol they are transporting. The development of atheroma (atherogenesis) narrows blood vessels, reduces the blood supply and leads to cardiovascular diseases. According to the World Health Organization (WHO), cardiovascular diseases are the leading cause of death, which has been especially boosted since the COVID-19 pandemic. There is a variety of contributors to atherosclerosis, including lifestyle factors and genetic predisposition. Antioxidant diets and recreational exercises act as atheroprotectors and can retard atherogenesis. The search for molecular markers of atherogenesis and atheroprotection for predictive, preventive and personalized medicine appears to be the most promising direction for the study of atherosclerosis. In this work, we have analyzed 1068 human genes associated with atherogenesis, atherosclerosis and atheroprotection. The hub genes regulating these processes have been found to be the most ancient. In silico analysis of all 5112 SNPs in their promoters has revealed 330 candidate SNP markers, which statistically significantly change the affinity of the TATA-binding protein (TBP) for these promoters. These molecular markers have made us confident that natural selection acts against underexpression of the hub genes for atherogenesis, atherosclerosis and atheroprotection. At the same time, upregulation of the one for atheroprotection promotes human health.

Age-related differences in physiology and survival of northern red-backed voles (Myodes rutilus) in captivity.

Age-related deterioration of physiological functions is one of the most evident manifestations of ageing. In wild populations of some species, including murid rodents, lifespans are substantially modified by environmental signals that affect an individual's response to such challenges as unfavourable climatic conditions, parasitic load etc. But the real impact of ageing on natural mortality of most species remains obscure. To clarify how age affects the responsiveness of organisms to environmental challenges, we performed longitudinal laboratory observations of wild-derived northern red-backed voles (Myodes rutilus). We fixed individual longevity and measured metabolic indexes (basal and maximal metabolic rates), ability to maintain body temperature under acute cooling, plasma corticosterone, indexes of acquired and innate immunity in the same individuals of 3-4, 6-7 and 9-10 months old. The maximum estimated lifespan was about 2 years 8 months, which is considerably older than in nature, but less than 30% of individuals passed the one-year milestone. Regardless of the intense mortality, in the first year of life, animals did not demonstrate any age-related deterioration in physiological functions, except leucocyte number. No consistency in any individual physiological index was found. As the individual longevity of red-backed voles varied between years of captivity, we suggest that the welfare and lifespan of wild animals in captivity may be affected by the environmental conditions in the period preceding removal of the animal from the wild.

Fathers and sons: Physiological stress in male Zaisan mole voles, Ellobius tancrei.

The social environment can be stressful for at least some group members, resulting in elevated levels of glucocorticoid stress hormones (GC). Patterns of the relationships between social rank and GC levels vary between species. In carnivores, primates and birds that live in permanent cooperative groups, helpers do not usually display physiological indicators of stress. Very little is known about status-related GC differences within cooperative groups of rodents. In this laboratory study, we compared GC concentrations in dominant (fathers) and subordinate (natal sons) males of a cooperative subterranean vole, Ellobius tancrei. The assessment of adrenocortical activity by measuring urine glucocorticoid metabolites (UGM) was previously validated for this species through an ACTH challenge test. We observed clear peaks of UGM in the second or third urine samples taken after the administration of ACTH (lag time equal to 2.5-3 h). Thus, UGM is suitable to estimate physiological stress in Ellobius. Postpubertal sons living in natal groups had significantly higher UGM concentrations than their fathers. The average UGM levels of sons were positively associated with their ages and paternal body masses, and negatively associated with paternal ages. Hence, son-father interactions rather than just younger ages of sons appear to contribute to GC differences. The revealed pattern was not consistent with that reported for most cooperative species from other taxa, highlighting the importance of comparative studies.

Effects of parasites and antigenic challenge on metabolic rates and thermoregulation in northern red-backed voles (Myodes rutilus).

Perturbations in host energetics are considered to be an essential pathway for parasite impact on host fitness. However, direct estimations of parasite-induced variations in basal metabolic rates of vertebrate hosts have so far provided contradictory results. The energy requirements of immunity and other vital functions may be compromised in energy-demanding conditions in comparison to comfortable conditions; therefore, in our study performed on the wild red-backed vole, Myodes rutilus, we compared the values of indices that reflect metabolic and thermoregulatory responses to acute cooling in individuals that had been naturally infected by gut helminths or Ixodes persulcatus taiga ticks to individuals with no signs of infestation. To consider the possible effects of an acquired immune response on host energetics, we also injected some of the tested individuals with sheep red blood cells (SRBC). Red-backed voles infected by the nematode Heligmosomum mixtum injected with SRBC showed significantly lower cold-induced maximum oxygen consumption than the saline control. Additionally, individuals infected with H. mixtum showed significantly lower oxygen consumption during the final minute of the 15-min acute cooling period and a significantly greater decline in body temperature than individuals free from helminths. In individuals concurrently infected by H. mixtum and the cestodes Arostrilepis horrida, these indices did not differ from helminth-free individuals. The number of ticks simultaneously parasitizing the voles at the moment of capture correlated positively with their SMR. Our results suggest that even natural parasites produce deleterious effects on host aerobic capacity and thermoregulatory abilities, although the effects of different parasites might not be additive.

Effect of Domain Structure and Dielectric Interlayer on Switching Speed of Ferroelectric Hf0.5Zr0.5O2 Film.

The nanosecond speed of information writing and reading is recognized as one of the main advantages of next-generation non-volatile ferroelectric memory based on hafnium oxide thin films. However, the kinetics of polarization switching in this material have a complex nature, and despite the high speed of internal switching, the real speed can deteriorate significantly due to various external reasons. In this work, we reveal that the domain structure and the dielectric layer formed at the electrode interface contribute significantly to the polarization switching speed of 10 nm thick Hf0.5Zr0.5O2 (HZO) film. The mechanism of speed degradation is related to the generation of charged defects in the film which accompany the formation of the interfacial dielectric layer during oxidization of the electrode. Such defects are pinning centers that prevent domain propagation upon polarization switching. To clarify this issue, we fabricate two types of similar W/HZO/TiN capacitor structures, differing only in the thickness of the electrode interlayer, and compare their ferroelectric (including local ferroelectric), dielectric, structural (including microstructural), chemical, and morphological properties, which are comprehensively investigated using several advanced techniques, in particular, hard X-ray photoelectron spectroscopy, high-resolution transmission electron microscopy, energy dispersive X-ray spectroscopy, X-ray diffraction, and electron beam induced current technique.

Polarization Switching Kinetics in Thin Ferroelectric HZO Films.

Ferroelectric polycrystalline HfO2 thin films are the most promising material for the implementation of novel non-volatile ferroelectric memories because of their attractive properties, such as compatibility with modern Si technology, perfect scalability, low power consumption and high endurance. However, for the commercialization of ferroelectric memory, some crucial aspects of its operation should be addressed, including the polarization switching mechanism that determines the switching speed. Although several reports on polarization switching kinetics in HfO2-based layers already exist, the physical origin of retardation behavior of polarization switching at the low and medium switching fields remains unclear. In this work, we examine several models of switching kinetics that can potentially explain or describe retardation behavior observed in experimental switching kinetics for Hf0.5Zr0.5O2 (HZO)-based capacitors and propose a new model. The proposed model is based on a statistical model of switching kinetics, which has been significantly extended to take into account the specific properties of HZO. The model includes contributions of the depolarization field and the built-in internal field originating from the charge injection into the functional HZO layer during the read procedure as well as in-plane inhomogeneity of the total electric field in ferroelectric. The general model of switching kinetics shows excellent agreement with the experimental results.

Ferroelectric Second-Order Memristor.

While the conductance of a first-order memristor is defined entirely by the external stimuli, in the second-order memristor it is governed by the both the external stimuli and its instant internal state. As a result, the dynamics of such devices allows to naturally emulate the temporal behavior of biological synapses, which encodes the spike timing information in synaptic weights. Here, we demonstrate a new type of second-order memristor functionality in the ferroelectric HfO2-based tunnel junction on silicon. The continuous change of conductance in the p+-Si/Hf0.5Zr0.5O2/TiN tunnel junction is achieved via the gradual switching of polarization in ferroelectric domains of polycrystalline Hf0.5Zr0.5O2 layer, whereas the combined dynamics of the built-in electric field and charge trapping/detrapping at the defect states at the bottom Si interface defines the temporal behavior of the memristor device, similar to synapses in biological systems. The implemented ferroelectric second-order memristor exhibits various synaptic functionalities, such as paired-pulse potentiation/depression and spike-rate-dependent plasticity, and can serve as a building block for the development of neuromorphic computing architectures.