Different vulnerability of fast and slow cortical oscillations to suppressive effect of spreading depolarization: state-dependent features potentially relevant to pathogenesis of migraine aura.

BACKGROUND: Spreading depolarization (SD), underlying mechanism of migraine aura and potential activator of pain pathways, is known to elicit transient local silencing cortical activity. Sweeping across the cortex, the electrocorticographic depression is supposed to underlie spreading negative symptoms of migraine aura. Main information about the suppressive effect of SD on cortical oscillations was obtained in anesthetized animals while ictal recordings in conscious patients failed to detect EEG depression during migraine aura. Here, we investigate the suppressive effect of SD on spontaneous cortical activity in awake animals and examine whether the anesthesia modifies the SD effect. METHODS: Spectral and spatiotemporal characteristics of spontaneous cortical activity following a single unilateral SD elicited by amygdala pinprick were analyzed in awake freely behaving rats and after induction of urethane anesthesia. RESULTS: In wakefulness, SD transiently suppressed cortical oscillations in all frequency bands except delta. Slow delta activity did not decline its power during SD and even increased it afterwards; high-frequency gamma oscillations showed the strongest and longest depression under awake conditions. Unexpectedly, gamma power reduced not only during SD invasion the recording cortical sites but also when SD occupied distant subcortical/cortical areas. Contralateral cortex not invaded by SD also showed transient depression of gamma activity in awake animals. Introduction of general anesthesia modified the pattern of SD-induced depression: SD evoked the strongest cessation of slow delta activity, milder suppression of fast oscillations and no distant changes in gamma activity. CONCLUSION: Slow and fast cortical oscillations differ in their vulnerability to SD influence, especially in wakefulness. In the conscious brain, SD produces stronger and spatially broader depression of fast cortical oscillations than slow ones. The frequency-specific effects of SD on cortical activity of awake brain may underlie some previously unexplained clinical features of migraine aura.

On the Benefits of Listen before Talk Scheme for NB-Fi Networks.

NB-Fi (Narrow Band Fidelity) is a promising protocol for low-power wide-area networks. NB-Fi networks use license-exempt Industrial, Scientific, and Medical (ISM) bands and, thus, NB-Fi devices can work in two modes: with and without Listen Before Talk (LBT). This paper compares these modes with different implementations of LBT in terms of packet loss rate (PLR), delay, energy consumption, and throughput. Interestingly, in some scenarios, the results contradict expectations from the classic papers on channel access because of the peculiarities of the NB-Fi technology. These contradictions are explained in the paper. The results show that LBT can significantly improve all the considered performance indicators when the network load exceeds 40 packets per second. With extensive simulation, we show that in a small NB-Fi network, the optimal PLR, delay, and energy consumption are obtained with the implementation of LBT that corresponds to non-persistent CSMA. In a large NB-Fi network, where some devices can be hidden from others, the best strategy to improve PLR, delay, throughput, and energy consumption is to use the implementation of LBT that corresponds to p-persistent CSMA.

Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes.

BACKGROUND: RNA-seq has become a standard technology to quantify mRNA. The measured values usually vary by several orders of magnitude, and while the detection of differences at high values is statistically well grounded, the significance of the differences for rare mRNAs can be weakened by the presence of biological and technical noise. RESULTS: We have developed a method for cleaning RNA-seq data, which improves the detection of differentially expressed genes and specifically genes with low to moderate transcription. Using a data modeling approach, parameters of randomly distributed mRNA counts are identified and reads, most probably originating from technical noise, are removed. We demonstrate that the removal of this random component leads to the significant increase in the number of detected differentially expressed genes, more significant pvalues and no bias towards low-count genes. CONCLUSION: Application of RNAdeNoise to our RNA-seq data on polysome profiling and several published RNA-seq datasets reveals its suitability for different organisms and sequencing technologies such as Illumina and BGI, shows improved detection of differentially expressed genes, and excludes the subjective setting of thresholds for minimal RNA counts. The program, RNA-seq data, resulted gene lists and examples of use are in the supplementary data and at https://github.com/Deyneko/RNAdeNoise .

Development of dual reporter vector system for estimating translational activity of regulatory elements.

BACKGROUND: For the needs of modern biotechnology, a quantitative approach to the control of regulatory elements at all stages of gene expression has long become indispensable. Such a control regime is impossible without a quantitative analysis of the role of each regulatory element or pattern used. Therefore, it seems important to modify and develop the accuracy, reproducibility, and availability of methods for quantifying the contribution of each regulatory code to the implementation of genetic information. RESULTS: A new vector system for transient expression in plants is described; this system is intended for quantitative analysis of the contribution of regulatory elements to transcription and translation efficiencies. The proposed vector comprises two expression cassettes carrying reporter genes (of the Clostridium thermocellum thermostable lichenase and E. coli ß-glucuronidase) under the control of different promoters. Herewith we also propose a new method for quantification of the effect of tested regulatory elements on expression, which relies on assessment of the enzyme activities of reporter proteins taking into account the transcription of their genes. CONCLUSIONS: In our view, this approach makes it possible to precisely determine the amounts of reporter proteins and their transcripts at all stages of expression. The efficiency of the proposed system has been validated by the analysis of the roles of known translation enhancers at the stages of transcription and translation.

Mechanism of chiral recognition by enantiomorphous cytosine crystals during enantiomer adsorption.

The quest to understand why life exhibits chirality has been far from successful. In the terrestrial theory of chirality emergence in living matter, one of the main possible mechanisms is the chiral recognition of organic molecules by enantiomorphic crystals. In this work, we studied the ability of enantiomorphic cytosine crystals, obtained by Viedma ripening, for chiral recognition by enantiomers adsorption. For this, we used MD calculations, inverse gas chromatography, and adsorption from solutions. The difference between the isotherms of enantiomers was determined using a t-test. We found that cytosine crystals were capable of chiral recognition only when the adsorbate concentration on the surface was sufficient for lateral interactions leading to layer formation. In order to approximate adsorption isotherms, Langmuir, Freundlich, BET, and Fowler-Guggenheim equations were used. The difference in lateral interactions between menthol enantiomers during their adsorption from a solution in n-heptane was established. A mechanism of chiral recognition of the adsorbed substance by cytosine crystals was proposed. The conditions under which chiral recognition could proceed were determined. We observed that, upon adsorption from a solution, chiral recognition manifested itself at higher coverages than in MD simulations. This was caused by the competitive adsorption of the solvent. The results obtained show that adsorption on enantiomorphic crystals could be the source of the first minute enantiomeric excess, providing an opportunity to understand the origin of chiral imbalance.

The features that distinguish lichenases from other polysaccharide-hydrolyzing enzymes and the relevance of lichenases for biotechnological applications.

The main specific features of ß-1,3-1,4-glucanases (or lichenases, EC 3.2.1.73), the enzymes that in a strictly specific manner hydrolyze ß-glucans of many cereal species and lichens containing ß-1,3 and ß-1,4 bonds, are reviewed as well as the current strategies used for their protein design, which have been successfully applied to make lichenases more attractive and promising for biocatalytic conversion of biomass, in particular, in the areas of their biotechnological application, such as brewing industry, animal feed manufacture, and biofuel production, which will in future allow these technologies to be economically and ecologically beneficial.

Computational and Experimental Tools to Monitor the Changes in Translation Efficiency of Plant mRNA on a Genome-Wide Scale: Advantages, Limitations, and Solutions.

The control of translation in the course of gene expression regulation plays a crucial role in plants' cellular events and, particularly, in responses to environmental factors. The paradox of the great variance between levels of mRNAs and their protein products in eukaryotic cells, including plants, requires thorough investigation of the regulatory mechanisms of translation. A wide and amazingly complex network of mechanisms decoding the plant genome into proteome challenges researchers to design new methods for genome-wide analysis of translational control, develop computational algorithms detecting regulatory mRNA contexts, and to establish rules underlying differential translation. The aims of this review are to (i) describe the experimental approaches for investigation of differential translation in plants on a genome-wide scale; (ii) summarize the current data on computational algorithms for detection of specific structure⁻function features and key determinants in plant mRNAs and their correlation with translation efficiency; (iii) highlight the methods for experimental verification of existed and theoretically predicted features within plant mRNAs important for their differential translation; and finally (iv) to discuss the perspectives of discovering the specific structural features of plant mRNA that mediate differential translation control by the combination of computational and experimental approaches.

PASylation technology improves recombinant interferon-ß1b solubility, stability, and biological activity.

Recombinant interferon-ß1b (IFN-ß1b) is an effective remedy against multiple sclerosis and other diseases. However, use of small polypeptide (molecular weight is around 18.5 kDa) is limited due to poor solubility, stability, and short half-life in systemic circulation. To solve this problem, we constructed two variants of PASylated IFN-ß1b, with PAS sequence at C- or N-terminus of IFN-ß1b. The PAS-modified proteins demonstrated 4-fold increase in hydrodynamic volume of the molecule combined with 2-fold increase of in vitro biological activity, as well as advanced stability and solubility of the protein in solution as opposed to unmodified IFN-ß1b. Our results demonstrate that PASylation has a positive impact on stability, solubility, and functional activity of IFN-ß1b and potentially might improve pharmacokinetic properties of the molecule as a therapeutic agent.

The novel HLA-DPB1*04:02:01:44 allele identified in a volunteer bone marrow donor.

Nucleotide substitution in the intron 2 of HLA-DPB1*04:02:01:01 results in a novel allele, HLA-DPB1*04:02:01:44.

The influence of long-term housing in enriched environment on behavior of normal rats and subjected to neonatal pro-inflammatory challenge.

It is well known that neonatal pro-inflammatory challenge (NPC) acquire a predisposition to the development of a number of neuropsychiatric diseases: depression, anxiety disorders, autism, attention deficit hyperactivity disorder. Symptoms of these diseases can manifest themselves in adulthood and adolescent after repeated exposure to negative influences. Preventing the development of the negative consequences of NPC is one of the main tasks for researchers. The exposure to an enriched environment (EE) was shown to have anxiolytic, anti-depressive, and pro-cognitive effects. The present work was aimed to investigate the effects of the long-term EE on anxious-depressive and conditioned fear behavior in normal male and female rats and subjected to NPC. The NPC was induced by subcutaneous administration of lipopolysaccharide (LPS, 50 µg/kg) on 3d and 5th PNDs. The control animals received saline (SAL). The rats were placed in the EE from 25 to 120 PND. Animals housed in the standard conditions (STAND) served as controls. In adult female and male rats of the STAND groups, LPS did not affect the anxiety, depressive-like behavior and conditioned fear. The EE increased motor and search activity in males and females. In the open field, the EE reduced anxiety in males of the SAL and LPS groups and in females of SAL groups compared to the STAND housed animals. In the elevated plus maze, the EE decreased anxiety only in males of the SAL group. In the sucrose preference test, the EE did not change sucrose consumption in males and females of SAL and LPS groups, while, in the forced swimming test, the EE reduced depressive-like behavior in females of both SAL and LPS groups. The enrichment decreased the contextual conditioned fear in male and female of SAL groups, but not of the LPS group, and did not affect the cue conditioned fear. The corticosterone reactivity to the forced swimming stress increased in males of the EE groups. The basal level of IL-1beta in blood serum decreased in males of the SAL-EE group. Thus, the EE reduced anxiety in males, depressive-like behavior in females, and contextual conditioned fear in males and females compared to the STAND housed animals. Although the NPC did not affect these behaviors in the STAND groups, LPS prevented the beneficial EE effects on anxiety and conditioned fear. The opposing effects of LPS were dependent on sex and type of testing.

Amide-Containing Bottlebrushes via Continuous-Flow Photoiniferter Reversible Addition-Fragmentation Chain Transfer Polymerization: Micellization Behavior.

Herein, a series of ternary amphiphilic amide-containing bottlebrushes were synthesized by photoiniferter (PI-RAFT) polymerization of macromonomers in continuous-flow mode using trithiocarbonate as a chain transfer agent. Visible light-mediated polymerization of macromonomers under mild conditions enabled the preparation of thermoresponsive copolymers with low dispersity and high yields in a very short time, which is not typical for the classical reversible addition-fragmentation chain transfer process. Methoxy oligo(ethylene glycol) methacrylate and alkoxy(C12-C14) oligo(ethylene glycol) methacrylate were used as the basic monomers providing amphiphilic and thermoresponsive properties. The study investigated how modifying comonomers, acrylamide (AAm), methacrylamide (MAAm), and N-methylacrylamide (-MeAAm) affect the features of bottlebrush micelle formation, their critical micelle concentration, and loading capacity for pyrene, a hydrophobic drug model. The results showed that the process is scalable and can produce tens of grams of pure copolymer per day. The unmodified copolymer formed unimolecular micelles at temperatures below the LCST in aqueous solutions, as revealed by DLS and SLS data. The incorporation of AAm, MAAm, and N-MeAAm units resulted in an increase in micelle aggregation numbers. The resulting bottlebrushes formed uni- or bimolecular micelles at extremely low concentrations. These micelles possess a high capacity for loading pyrene, making them a promising choice for targeted drug delivery.

Nature-based solutions can help reduce the impact of natural hazards: A global analysis of NBS case studies.

The knowledge derived from successful case studies can act as a driver for the implementation and upscaling of nature-based solutions (NBS). This work reviewed 547 case studies to gain an overview of NBS practices and their role in reducing the adverse impact of natural hazards and climate change. The majority (60 %) of case studies are situated in Europe compared with the rest of the world where they are poorly represented. Of 547 case studies, 33 % were green solutions followed by hybrid (31 %), mixed (27 %), and blue (10 %) approaches. Approximately half (48 %) of these NBS interventions were implemented in urban (24 %), and river and lake (24 %) ecosystems. Regarding the scale of intervention, 92 % of the case studies were operationalised at local (50 %) and watershed (46 %) scales while very few (4 %) were implemented at the landscape scale. The results also showed that 63 % of NBS have been used to deal with natural hazards, climate change, and loss of biodiversity, while the remaining 37 % address socio-economic challenges (e.g., economic development, social justice, inequality, and cohesion). Around 88 % of NBS implementations were supported by policies at the national level and the rest 12 % at local and regional levels. Most of the analysed cases contributed to Sustainable Development Goals 15, 13, and 6, and biodiversity strategic goals B and D. Case studies also highlighted the co-benefits of NBS: 64 % of them were environmental co-benefits (e.g., improving biodiversity, air and water qualities, and carbon storage) while 36 % were social (27 %) and economic (9 %) co-benefits. This synthesis of case studies helps to bridge the knowledge gap between scientists, policymakers, and practitioners, which can allow adopting and upscaling of NBS for disaster risk reduction and climate change adaptation and enhance their preference in decision-making processes.

A Molecular Orchestration of Plant Translation under Abiotic Stress.

The complexities of translational strategies make this stage of implementing genetic information one of the most challenging to comprehend and, simultaneously, perhaps the most engaging. It is evident that this diverse range of strategies results not only from a long evolutionary history, but is also of paramount importance for refining gene expression and metabolic modulation. This notion is particularly accurate for organisms that predominantly exhibit biochemical and physiological reactions with a lack of behavioural ones. Plants are a group of organisms that exhibit such features. Addressing unfavourable environmental conditions plays a pivotal role in plant physiology. This is particularly evident with the changing conditions of global warming and the irrevocable loss or depletion of natural ecosystems. In conceptual terms, the plant response to abiotic stress comprises a set of elaborate and intricate strategies. This is influenced by a range of abiotic factors that cause stressful conditions, and molecular genetic mechanisms that fine-tune metabolic pathways allowing the plant organism to overcome non-standard and non-optimal conditions. This review aims to focus on the current state of the art in the field of translational regulation in plants under abiotic stress conditions. Different regulatory elements and patterns are being assessed chronologically. We deem it important to focus on significant high-performance techniques for studying the genetic information dynamics during the translation phase.

Spreading depolarization induced by amygdala micro-injury prevents disruption of fear memory extinction in rats.

Spreading depolarization (SD), a self-propagating wave of near-complete breakdown of the transmembrane ion gradients with water influx, regularly occurs in traumatized human brain. Here, we investigated long-term neurobehavioral consequences of injury-triggered SDs. Recently, we revealed that SD is reliably triggered by micro-injury of the amygdala, a key brain structure involved in fear processing. Using the classical Pavlovian fear conditioning paradigm, we investigated effects of the post-retrieval amygdala micro-injury and associated SD on fear memory in rats. We found that neither SD nor micro-injury alone affect fear response 24 h later but profoundly change it in subsequent extinction phase. If bilateral injury of the amygdala did not induce SD, fear extinction was severely impaired, while conditioned fear in rats with the identical amygdala injury triggering SD was successfully extinguished similarly to naïve rats. Our study provides first experimental evidence for involvement of injury-induced SD in extinction of traumatic fear memory.

Region-Specific Vulnerability of the Amygdala to Injury-Induced Spreading Depolarization.

Spreading depolarization (SD), a self-propagated wave of transient depolarization, regularly occurs in the cortex after acute brain insults and is now referred as an important diagnostic and therapeutic target in patients with acute brain injury. Here, we show that the amygdala, the limbic structure responsible for post-injury neuropsychological symptoms, exhibits strong regional heterogeneity in vulnerability to SD with high susceptibility of its basolateral (BLA) region and resilience of its centromedial (CMA) region to triggering SD by acute focal damage. The BLA micro-injury elicited SD twice as often compared with identical injury of the CMA region (71% vs. 33%). Spatiotemporal features of SDs triggered in the amygdala indicated diverse patterns of the SD propagation to the cortex. Our results suggest that even relatively small cerebral structures can exhibit regional gradients in their susceptibility to SD and the heterogeneity may contribute to the generation of complex SD patterns in the injured brain.

HLA Genotypes in Patients with Infection Caused by Different Strains of SARS-CoV-2.

The aggressive infectious nature of SARS-CoV-2, its rapid spread, and the emergence of mutations necessitate investigation of factors contributing to differences in SARS-CoV-2 susceptibility and severity. The role of genetic variations in the human HLA continues to be studied in various populations in terms of both its effect on morbidity and clinical manifestation of illness. The study included 484 COVID-19 convalescents (northwest Russia residents of St. Petersburg). Cases in which the responsible strain was determined were divided in two subgroups: group 1 (n = 231) had illness caused by genovariants unrelated to variant of concern (VOC) strains; and group 2 (n = 80) had illness caused by the delta (B.1.617.2) VOC; and a control group (n = 1456). DNA typing (HLA-A, B, DRB1) was performed at the basic resolution level. HLA-A*02 was associated with protection against infection caused by non-VOC SARS-CoV-2 genetic variants only but not against infection caused by delta strains. HLA-A*03 was associated with protection against infection caused by delta strains; and allele groups associated with infection by delta strains were HLA-A*30, B*49, and B*57. Thus, in northwest Russia, HLA-A*02 was associated with protection against infection caused by non-VOC SARS-CoV-2 genetic variants but not against delta viral strains. HLA-A*03 was associated with a reduced risk of infection by delta SARS-CoV-2 strains. HLA-A*30, HLA-B*49, and HLA-B*57 allele groups were predisposing factors for infection by delta (B.1.617.2) strains.

Modulation of the Translation Efficiency of Heterologous mRNA and Target Protein Stability in a Plant System: The Case Study of Interferon-αA.

A broad and amazingly intricate network of mechanisms underlying the decoding of a plant genome into the proteome forces the researcher to design new strategies to enhance both the accumulation of recombinant proteins and their purification from plants and to improve the available relevant strategies. In this paper, we propose new approaches to optimize a codon composition of target genes (case study of interferon-αA) and to search for regulatory sequences (case study of 5'UTR), and we demonstrated their effectiveness in increasing the synthesis of recombinant proteins in plant systems. In addition, we convincingly show that the approach utilizing stabilization of the protein product according to the N-end rule or a new protein-stabilizing partner (thermostable lichenase) is sufficiently effective and results in a significant increase in the protein yield manufactured in a plant system. Moreover, it is validly demonstrated that thermostable lichenase as a protein-stabilizing partner not only has no negative effect on the target protein activity (interferon-αA) integrated in its sequence, but rather enhances the accumulation of the target protein product in plant cells. In addition, the retention of lichenase enzyme activity and interferon biological activity after the incubation of plant protein lysates at 65 °C and precipitation of nontarget proteins with ethanol is applicable to a rapid and inexpensive purification of fusion proteins, thereby confirming the utility of thermostable lichenase as a protein-stabilizing partner for plant systems.

Response of Transgenic Potato Plants Expressing Heterologous Genes of ∆9- or ∆12-Acyl-lipid Desaturases to Phytophthora infestans Infection.

Late blight is one of the most economically important diseases affecting potato and causing a significant loss in yield. The development of transgenic potato plants with enhanced resistance to infection by Phytophthora infestans may represent a possible approach to solving this issue. A comparative study of the leaf response in control potato plants (S.tuberosum L. cultivar Skoroplodnyi), control transgenic plants expressing the reporter gene of thermostable lichenase (transgenic licBM3 line) and transgenic plants expressing cyanobacterial hybrid genes ∆9-acyl-lipid desaturase (transgenic desC lines) and ∆12-acyl-lipid desaturase (transgenic desA lines) to infection with P. infestans has been performed. The expression of desaturase genes in potato plants enhanced their tolerance to potato late blight agents as compared with the control. The lipid peroxidation level raised in the leaves of the control and transgenic desA plants on third day after inoculation with P. infestans zoospores and remained the same in the transgenic desC plants. The number of total phenolic compounds was increased as early as on the second day after infection in all studied variants and continued to remain the same, except for transgenic desC plants. Accumulation of flavonoids, the main components of the potato leaf phenolic complex, raised on the second day in all studied variants, remained unchanged on the third day in the control plants and decreased in most transgenic plants expressing desaturase genes. The results obtained in our study demonstrate that the expression of genes of Δ9- and Δ12-acyl-lipid desaturases in potato plants enhanced their resistance to P. infestans as compared with the control non-transgenic plants due to concomitant accumulation of phenolic compounds, including flavonoids, in the leaves. All these changes were more pronounced in transgenic desC plants, which indicates that the Δ9-acyllipid desaturase gene appears to be a potential inducer of the production of biological antioxidants in plant cells.

DeepLabStream enables closed-loop behavioral experiments using deep learning-based markerless, real-time posture detection.

In general, animal behavior can be described as the neuronal-driven sequence of reoccurring postures through time. Most of the available current technologies focus on offline pose estimation with high spatiotemporal resolution. However, to correlate behavior with neuronal activity it is often necessary to detect and react online to behavioral expressions. Here we present DeepLabStream, a versatile closed-loop tool providing real-time pose estimation to deliver posture dependent stimulations. DeepLabStream has a temporal resolution in the millisecond range, can utilize different input, as well as output devices and can be tailored to multiple experimental designs. We employ DeepLabStream to semi-autonomously run a second-order olfactory conditioning task with freely moving mice and optogenetically label neuronal ensembles active during specific head directions.

A high throughput assay of lichenase activity with Congo red dye in plants.

BACKGROUND: Since the beginning of the use of reporter proteins for expression analysis, a variety of approaches have been developed and proposed; both qualitative and quantitative. The lack of simple methods for direct observation of gene expression in living organisms makes it necessary to continue to propose new methods. In this work, we consider a method for the quantitative analysis of the expression of thermostable lichenase from Clostridium thermocellum used as a sensitive reporter protein. RESULTS: In this study, we report the design a high throughput fluorometric method for quantification of thermostable lichenase C. thermocellum using Congo red and further experimental verification of its relevance and efficiency in assessment of the functional role of regulatory sequences in the plant cell. CONCLUSIONS: The specific interaction between the dye Congo red and [Formula: see text]-D-glucans formed the background for designing a high-throughput fluorometric assay for quantification of C. thermocellum thermostable lichenase as a reporter protein for plants. This assay (i) makes it possible to precisely measure the amount of reporter protein in a plant sample; (ii) has shown a high sensitivity for quantification of thermostable lichenase; (iii) is more time- and cost-efficient as compared with the Somogyi-Nelson assay; and (iv) is to the least degree dependent on the presence of the tested buffer components as compared with the Somogyi-Nelson assay.