Biochemical Processes Research Articles

Microbial central carbon metabolism in a tidal freshwater marsh and an upland mixed conifer soil under oxic and anoxic conditions.

The central carbon (C) metabolic network is responsible for most of the production of energy and biosynthesis in microorganisms and is therefore key to a mechanistic understanding of microbial life in soil communities. Many upland soil communities have shown a relatively high C flux through the pentose phosphate (PP) or the Entner-Doudoroff (ED) pathway, thought to be related to oxidative damage control. We tested the hypothesis that the metabolic organization of the central C metabolic network differed between two ecosystems, an anoxic marsh soil and oxic upland soil, and would be affected by altering oxygen concentrations. We expected there to be high PP/ED pathway activity under high oxygen concentrations and in oxic soils and low PP/ED activity in reduced oxygen concentrations and in marsh soil. Although we found high PP/ED activity in the upland soil and low activity in the marsh soil, lowering the oxygen concentration for the upland soil did not reduce the relative PP/ED pathway activity as hypothesized, nor did increasing the oxygen concentration in the marsh soil increase the PP/ED pathway activity. We speculate that the high PP/ED activity in the upland soil, even when exposed to low oxygen concentrations, was related to a high demand for NADPH for biosynthesis, thus reflecting higher microbial growth rates in C-rich soils than in C-poor sediments. Further studies are needed to explain the observed metabolic diversity among soil ecosystems and determine whether it is related to microbial growth rates.IMPORTANCEWe observed that the organization of the central carbon (C) metabolic processes differed between oxic and anoxic soil. However, we also found that the pentose phosphate pathway/Entner-Doudoroff (PP/ED) pathway activity remained high after reducing the oxygen concentration for the upland soil and did not increase in response to an increase in oxygen concentration in the marsh soil. These observations contradicted the hypothesis that oxidative stress is a main driver for high PP/ED activity in soil communities. We suggest that the high PP/ED activity and NADPH production reflect higher anabolic activities and growth rates in the upland soil compared to the anaerobic marsh soil. A greater understanding of the molecular and biochemical processes in soil communities is needed to develop a mechanistic perspective on microbial activities and their relationship to soil C and nutrient cycling. Such an increased mechanistic perspective is ecologically relevant, given that the central carbon metabolic network is intimately tied to the energy metabolism of microbes, the efficiency of new microbial biomass production, and soil organic matter formation.

ADVANCEMENTS IN UNDERSTANDING THE MOLECULAR MECHANISMS REGULATING URIC ACID METABOLISM IN THE INTESTINE

This review provides contemporary insights into the direct and indirect pathogenetic connections between purine compound metabolism and biochemical processes within the cells of the gastrointestinal system. A thorough analysis of recent publications from 2000 to 2024, sourced from databases including Scopus, PubMed, eLIIBRARY, and Google Scholar, was conducted. Uric acid serves as the end product of purine-containing compound catabolism. Its concentration is intricately regulated through the collaboration of the kidneys and gastrointestinal organs, namely the small intestine and liver. Gout, a chronic condition, emerges from the interplay between molecular genetic factors and external influences. Elevated levels of urates in the blood serum (hyperuricemia) and the deposition of sodium urate crystals in organs and tissues set off a cascade of inflammatory and fibrotic processes within mucosal, smooth muscle, parenchymal, and endothelial cells, including those within the gastrointestinal tract. Normally, a person excretes about 1.5 g of uric acid per day. Under physiological conditions, two-thirds of uric acid is excreted from the body by the kidneys, one-third through the intestines, and a small part is excreted with bile. The hypothesis that links the pathogenesis of hyperuricemia with “renal overload” suggests that the disease may develop as a result of impaired renal excretion with insufficient elimination of uric acid through the intestines. Part of uric acid transport systems actively works in hepatocytes and enterocytes, which determines its formation and clearance. Uric acid transporter proteins are divided into two categories: urate reabsorption transporters and urate excretion transporters, their expression is regulated by transcription factors, hormones and metabolites of intestinal microflora. The influence of intestinal microbiota on uric acid metabolism is related to its participation in purine metabolism, decomposition and elimination of uric acid with metabolites of intestinal flora and inhibition of gouty inflammation and is evaluated as a new therapeutic potential in gout and hyperuricemia, which allows to avoid kidney damage and urolithiasis.

Afforestation Enhances Potential Bacterial Metabolic Function without Concurrent Soil Carbon: A Case Study of Mu Us Sandy Land

Elucidating the impact of afforestation on soil bacterial community composition and its potential function in afforestation is imperative for comprehending the biochemical processes of land use change. This study employed high-throughput genomic sequencing to determine the bacterial phylogenetic assembly and assess functional groups following afforestation encompassing shrubland and woodland. Compared with non-afforested cropland, the soil organic carbon (SOC) remained unchanged, but significant alterations were observed in the bacterial composition and potential functions under afforestation. Afforestation enhanced bacterial diversity and even shifted the bacteria from the r- to K-strategy, as indicated by higher oligotroph/copiotroph ratios. Soil properties explained 66.45% and 68.9% of the total variation in bacterial community composition at the phylum level and the functional group. A 60.44% decrease in soil water content, a 3.82% increase in pH, a 7.5% increase in bulk density, and a 66.8% decrease in available phosphorus (AP) were the main soil factors affecting both bacterial community composition and functional traits in afforestation. In particular, lower available nutrients, AP, and nitrate nitrogen in afforestation drive the bacterial life history strategies. We conclude that changes in bacterial metabolic functions due to reduced soil available nutrients from dryland afforestation might be the main driver for microbial-inhibited SOC accumulation. These results could provide strong microbiological evidence to help further evaluate the importance of dryland afforestation.

Preservation of Bacillus subtilis' cellular liquid state at deep sub-zero temperatures in perchlorate brines.

Although a low temperature limit for life has not been established, it is thought that there exists a physical limit imposed by the onset of intracellular vitrification, typically occurring at ~-20 °C for unicellular organisms. Here, we show, through differential scanning calorimetry, that molar concentrations of magnesium perchlorate can depress the intracellular vitrification point of Bacillus subtilis cells to temperatures much lower than those previously reported. At 2.5 M Mg(ClO4)2, the peak vitrification temperature was lowered to -83 °C. Our results show that inorganic eutectic salts can in principle maintain liquid water in cells at much lower temperatures than those previously claimed as a lower limit to life, raising the prospects of active biochemical processes in low temperature natural settings. Our results may have implications for the habitability of Mars, where perchlorate salts are pervasive and potentially other terrestrial and extraterrestrial, cryosphere environments.

Magnetic Modulation of Biochemical Synthesis in Synthetic Cells.

Synthetic cells can be constructed from diverse molecular components, without the design constraints associated with modifying 'living' biological systems. This can be exploited to generate cells with abiotic components, creating functionalities absent in biology. One example is magnetic responsiveness, the activation and modulation of encapsulated biochemical processes using a magnetic field, which is absent from existing synthetic cell designs. This is a critical oversight, as magnetic fields are uniquely bio-orthogonal, noninvasive, and highly penetrative. Here, we address this by producing artificial magneto-responsive organelles by coupling thermoresponsive membranes with hyperthermic Fe3O4 nanoparticles and embedding them in synthetic cells. Combining these systems enables synthetic cell microreactors to be built using a nested vesicle architecture, which can respond to alternating magnetic fields through in situ enzymatic catalysis. We also demonstrate the modulation of biochemical reactions by using different magnetic field strengths and the potential to tune the system using different lipid compositions. This platform could unlock a wide range of applications for synthetic cells as programmable micromachines in biomedicine and biotechnology.

Loci cg06256735 and cg15815843 in the MFAP5 gene regulatory regions are hypomethylated in varicose veins apparently due to active demethylation.

Varicose vein disease (VVD) is a common health problem worldwide. Microfibril Associated Protein 5 (MFAP5) is one of the potential key players in its pathogenesis. Our previous microarray analysis revealed the cg06256735 and cg15815843 loci in the regulatory regions of the MFAP5 gene as hypomethylated in varicose veins which correlated with its up-regulation. The aim of this work was to validate preliminary microarray data, estimate the level of 5-hydroxymethylcytosine (5hmC) at these loci, and determine the methylation status of one of them in different layers of the venous wall. For this, methyl- and hydroxymethyl-sensitive restriction techniques were used followed by real-time PCR and droplet digital PCR, correspondingly, as well as bisulfite pyrosequencing of +/- oxidized DNA. Our microarray data on hypomethylation at the cg06256735 and cg15815843 loci in whole varicose vein segments were confirmed and it was also demonstrated that the level of 5hmC at these loci is increased in VVD. Specifically, among other layers of the venous wall, t. intima is the main contributor to hypomethylation at the cg06256735 locus in varicose veins. Thus, it was shown that hypomethylation at the cg06256735 and cg15815843 loci takes place in VVD, with evidence to suggest that it happens through their active demethylation leading to up-regulation of the MFAP5 gene, and t. intima is most involved in this biochemical process.

ИЗУЧЕНИЕ ПРОЦЕССОВ КОМПЛЕКСООБРАЗОВАНИЯ В ПОЛИМЕРНЫХ БИОДЕГРАДИРУЕМЫХ КОМПОЗИЦИЯХ

One of the possible directions of the development of targeted substance delivery systems is the creation and introduction of biodegradable polymers into production. Their distinctive feature is that they are capable of spontaneously gradually degradation in the body due to natural biochemical processes. There is an increasing spread pharmaceutical form, which use similar excipients in their technology – medicinal ocular insert. Modified cellulose, gums and rare-cross-linked acrylic polymers are used to create a biodegradable matrix base. In terms of development approach, ocular inserts can be divided into two groups according to the principle of matrix biodegradation. In non-biodegradable composites, the effect of prolongation of the therapeutic effect is observed due to the release of the active substance from the non-decomposing matrix. This fact can be confirmed by both pharmacopoeial and non-pharmacopoeial methods. The classic tests regulated by the Pharmacopoeia of the XV edition include the "Dissolution" test (GPM.1.4.2.0014 "Dissolution of solid pharmaceutical dose forms"), and for non–pharmacopoeial ones – dialysis through a semipermeable membrane according to Kruvchinsky or using Franz's dialysis cells. The analysis of the kinetics of dissolution helps to determine and select the most suitable matrix-forming agent to be used in the composition with other substances in the composition of ocular insert. Ocular inserts with a biodegradable matrix have a second factor that affects the release of active substances – the formation of complexes or associates between parts of the matrix and the active ingredient molecules. These intermolecular compounds can indirectly prolong the effect of the drug. All features must be taken into account in the development of ocular inserts, since they, among other things, help to model fundamentally new ways of targeted delivery of substances. In this case, it is necessary to develop a test for the second modified release factor, which would reliably determine the presence of complexation processes within the selected ocular inserts model.

A Foam Line Position Detection Algorithm for A/O Pool Based on YOLOv5

During the biochemical pretreatment process of leachate in urban landfill sites, if the foam in the A/O pool is not promptly addressed, it can lead to overflow, posing hazards to the surrounding environment and personnel. Therefore, a real-time foam line detection algorithm based on YOLOv5x was proposed, which enhances feature information and improves anchor box regression prediction to accurately detect the position of foam lines. Firstly, in the preprocessing stage, employing a rectangular box to simultaneously label the foam line and the edge of the A/O pool within the same region, enhances the feature information of the foam line. Then, the C3NAM module was proposed, which applies weight sparse penalties to attention modules in the feature extraction section, to enhance the capability of extracting foam line features. Subsequently, a B-SPPCSPC module was proposed to enhance the fusion of shallow and deep feature information, addressing the issue of susceptibility to background interference during foam line detection. Next, the Focal_EIOU was introduced to ameliorate the issue of class imbalance in detection, providing more accurate bounding box predictions. Lastly, optimizing the detection layer scale improves the detection performance for smaller targets. The experimental results demonstrate that the accuracy of this algorithm reaches 98.9%, and the recall reaches 88.1%, with a detection frame rate of 26.2 frames per second, which can meet the actual detection requirements of real-world application scenarios.

Advanced Dressings for Chronic Wound Management.

Wound healing, particularly for chronic wounds, presents a considerable difficulty due to differences in biochemical and cellular processes that occur in different types of wounds. Recent technological breakthroughs have notably advanced the understanding of diagnostic and therapeutic approaches to wound healing. The evolution in wound care has seen a transition from traditional textile dressings to a variety of advanced alternatives, including self-healing hydrogels, hydrofibers, foams, hydrocolloids, environment responsive dressings, growth factor-based therapy, bioengineered skin substitutes, and stem cell and gene therapy. Technological advancements, such as 3D printing and electronic skin (e-skin) therapy, contribute to the customization of wound healing. Despite these advancements, effectively managing chronic wounds remains challenging. This necessitates the development of treatments that consider performance, risk-benefit balance, and cost-effectiveness. This review discusses innovative strategies for the healing of chronic wounds. Incorporating biomarkers into advanced dressings, coupled with corresponding biosensors and drug delivery formulations, enables the theranostic approach to the treatment of chronic wounds. Furthermore, integrating advanced dressings with power sources and user interfaces like near-field communication, radio frequency identification, and Bluetooth enhances real-time monitoring and on-demand drug delivery. It also provides a thorough evaluation of the advantages, patient compliance, costs, and durability of advanced dressings, emphasizing smart formulations and their preparation methods.

The role of reduced graphene oxide on mitigation of lead phytotoxicity in Triticum aestivum L.plants at morphological and physiological levels

Rapid global industrialization and an increase in population have enhanced the risk of heavy metals accumulation in plant bodies to disrupt the morphological, biochemical, and physiological processes of plants. To cope with this situation, reduced graphene oxide (rGO) NPs were used first time to mitigate abiotic stresses caused in plant. In this study, rGO NPs were synthesized and reduced with Tecoma stans plant leave extract through modified Hummer's methods. The well prepared rGO NPs were characterized by ultra-violet visible spectroscopy (UV–Vis), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), Zeta potential, and scanning electron microscopy (SEM). However, pot experiment was conducted with four different concentrations (15, 30, 60, 120 mg/L) of rGO NPs and three different concentrations (300, 500,700 mg/L) of lead (Pb) stress were applied. To observe the mitigative effects of rGO NPs, 30 mg/L of rGO NPs and 700 mg/L of Pb were used in combination. Changes in morphological and biochemical characteristics of wheat plants were observed for both Pb stress and rGO NPs treatments. Pb was found to inhibit the morphological and biochemical characteristics of plants. rGO NPs alone as well as in combination with Pb was found to increase the chlorophyll content of wheat plants. Under Pb stress conditions and rGO NPs treatments, antioxidant enzyme activities like ascorbate peroxidases (APX), superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were observed. Current findings revealed that greenly reduced graphene oxide NPs can effectively promote growth in wheat plants under Pb stress by elevating chlorophyll content of leaves, reducing the Pb uptake, and suppressing ROS produced due to Pb toxicity.

The cell as a semiotic system that realizes closure to efficient causation: The semiotic (M, R) system

Robert Rosen defines organisms as material systems closed to efficient causation, and proposes the replicative (M, R) system as a model for them. Recently, we presented a cell model that realizes Rosen's formal model, based on Hofmeyr's analysis of the functional organization of cell biochemistry and on Rosen's construction of the replication function. In this article we propose a cell model that, starting from the same biochemical processes, replaces the replication function with a set of semiotic relations between some of the elements that participate in cellular processes. The result is a cell model that constitutes a semiotic system that realizes closure to efficient causation: a semiotic (M, R) system. We compare the models of closure that correspond to the replicative (M, R) system and the semiotic (M, R) system. Additionally, we discuss the role that the genetic code and protein synthesis play in the semiotic closure to efficient causation. Finally, we outline the method to extend this analysis to more complex organisms.

Promoting Circular Economy of the Building Industry by the Use of Straw Bales: A Review

Over the past decade, the concept of a circular economy has increasingly gained attention as a framework for guiding businesses and policymakers. Given its significant environmental impact, the building industry plays a pivotal role in the transition toward a circular economy. To address this, our review proposes a bio-based building material, specifically straw bale, which elaborates on the circularity of bio-based buildings based on the 3R principles of a circular economy: reduce, reuse, and recycle. In terms of the “reduce” principle, straw-bale buildings can reduce construction waste, the environmental impact, energy requirements, and carbon emissions. Regarding the “reuse” principle, straw-bale buildings utilize agricultural waste resources and are easily disassembled due to their prefabrication. As for the “recycle” principle, straw-bale buildings can undergo physical, biological, and biochemical conversion processes (thermochemical conversion), yielding both wooden composite boards and potential biogas and biomass fuels for electricity and heating. This study evaluates the contribution of straw packaging construction and the use of straw as a raw material, using the 3R principles to determine future research opportunities for the construction industry to achieve a circular economy. The results of this study offer circular economy solutions and interdisciplinary research insights for researchers and practitioners interested in the building environment.

Lipid mediators in neutrophil biology: inflammation, resolution and beyond.

Acute inflammation is the body's first defense in response to pathogens or injury. Failure to efficiently resolve the inflammatory insult can severely affect tissue homeostasis, leading to chronic inflammation. Neutrophils play a pivotal role in eradicating infectious pathogens, orchestrating the initiation and resolution of acute inflammation, and maintaining physiological functions. The resolution of inflammation is a highly orchestrated biochemical process, partially modulated by a novel class of endogenous lipid mediators known as specialized pro-resolving mediators (SPMs). SPMs mediate their potent bioactions via activating specific cell-surface G protein-coupled receptors (GPCR). This review focuses on recent advances in understanding the multifaceted functions of SPMs, detailing their roles in expediting neutrophil apoptosis, promoting clearance by macrophages, regulating their excessive infiltration at inflammation sites, orchestrating bone marrow deployment, also enhances neutrophil phagocytosis and tissue repair mechanisms under both physiological and pathological conditions. We also focus on the novel role of SPMs in regulating bone marrow neutrophil functions, differentiation, and highlight open questions about SPMs' functions in neutrophil heterogeneity. SPMs play a pivotal role in mitigating excessive neutrophil infiltration and hyperactivity within pathological milieus, notably in conditions such as sepsis, cardiovascular disease, ischemic events, and cancer. This significant function highlights SPMs as promising therapeutic agents in the management of both acute and chronic inflammatory disorders.

Histology, fatty acid composition, antioxidant and glycolipid metabolism, and transcriptome analyses of the acute cold stress response in Phoxinus lagowskii

Water temperature is a crucial environmental factor that significantly affects the physiological and biochemical processes of fish. Due to the occurrence of cold events in aquaculture, it is imperative to investigate how fish respond to cold stress. This study aims to uncover the mechanisms responds to acute cold stress by conducting a comprehensive analysis of the histomorphology, glycolipid metabolic and antioxidant enzymes, fatty acid composition and transcriptome at three temperatures (16 °C, 10 °C and 4 °C) in Phoxinus lagowskii. Our results showed that cold stress not damaged muscle microstructure but caused autophagy (at 10 °C). In addition, serum glucose (Glu) and triglycerides (TG) increased during cold stress. The activities of reactive oxygen species (ROS), superoxide dismutase (SOD), catalase (CAT), fructose phosphokinase (PFK), hexokinase (HK), pyruvate kinase (PK), and malondialdehyde (MDA) content in muscle were measured and analyzed. During cold stress, superoxide dismutase and catalase activities increased, reactive oxygen species content decreased. No significant difference in Glutathione peroxidase (GPx) activity, malondialdehyde and total cholesterol (T-CHO) contents among groups. Phosphokinase and pyruvate kinase activities decreased, and HK activity increased during cold stress. Our study resulted in the identification of a total of 25,400 genes, with 2524 genes showing differential expression across different temperature treatments. Furthermore, KEGG pathway indicated that some pathways upregulated during light cold stress (at 10 °C, including autophagy, and AMP-activated protein kinase (AMPK) signaling pathway. Additionally, circadian rhythm is among the most enriched pathways in genes up-regulated during severe cold stress (at 4 °C). Our findings offer valuable insights into how cold-water fish respond to cold stress.

Implication of system xc− in neuroinflammation during the onset and maintenance of neuropathic pain

BackgroundDespite the high prevalence of neuropathic pain, treating this neurological disease remains challenging, given the limited efficacy and numerous side effects associated with current therapies. The complexity in patient management is largely attributed to an incomplete understanding of the underlying pathological mechanisms. Central sensitization, that refers to the adaptation of the central nervous system to persistent inflammation and heightened excitatory transmission within pain pathways, stands as a significant contributor to persistent pain. Considering the role of the cystine/glutamate exchanger (also designated as system xc−) in modulating glutamate transmission and in supporting neuroinflammatory responses, we investigated the contribution of this exchanger in the development of neuropathic pain.MethodsWe examined the implication of system xc− by evaluating changes in the expression/activity of this exchanger in the dorsal spinal cord of mice after unilateral partial sciatic nerve ligation. In this surgical model of neuropathic pain, we also examined the consequence of the genetic suppression of system xc− (using mice lacking the system xc− specific subunit xCT) or its pharmacological manipulation (using the pharmacological inhibitor sulfasalazine) on the pain-associated behavioral responses. Finally, we assessed the glial activation and the inflammatory response in the spinal cord by measuring mRNA and protein levels of GFAP and selected M1 and M2 microglial markers.ResultsThe sciatic nerve lesion was found to upregulate system xc− at the spinal level. The genetic deletion of xCT attenuated both the amplitude and the duration of the pain sensitization after nerve surgery, as evidenced by reduced responses to mechanical and thermal stimuli, and this was accompanied by reduced glial activation. Consistently, pharmacological inhibition of system xc− had an analgesic effect in lesioned mice.ConclusionTogether, these observations provide evidence for a role of system xc− in the biochemical processes underlying central sensitization. We propose that the reduced hypersensitivity observed in the transgenic mice lacking xCT or in sulfasalazine-treated mice is mediated by a reduced gliosis in the lumbar spinal cord and/or a shift in microglial M1/M2 polarization towards an anti-inflammatory phenotype in the absence of system xc−. These findings suggest that drugs targeting system xc− could contribute to prevent or reduce neuropathic pain.

Exploring the physicochemical properties of the integration of Tristearoyl uridine in Langmuir monolayers: An approach to cell membrane modeling for prodrugs

Understanding the mechanisms by which drugs interact with cell membranes is crucial for unraveling the underlying biochemical and biophysical processes that occur on the surface of these membranes. Our research focused on studying the interaction between an ester-type derivative of tristearoyl uridine and model cell membranes composed of lipid monolayers at the air-water interface. For that, we selected a specific lipid to simulate nontumorigenic cell membranes, namely 1,2-dihexadecanoyl-sn-glycero-3-phospho-l-serine. We noted significant changes in the surface pressure-area isotherms, with a noticeable shift towards larger areas, which was lower than expected for ideal mixtures, indicating monolayer condensation. Furthermore, the viscoelastic properties of the interfacial film demonstrated an increase in both the elastic and viscous parameters for the mixed film. We also observed structural alterations using vibrational spectroscopy, which revealed an increase in the all-trans to gauche conformers ratio. This confirmed the stiffening effect of the prodrug on the lipid monolayer. In summary, this study indicates that this lipophilic prodrug significantly impacts the lipid monolayer's thermodynamic, rheological, electrical, and molecular characteristics. This information is crucial for understanding how the drug interacts with specific sites on the cellular membrane. It also has implications for drug delivery, as the drug's passage into the cytosol may involve traversing the lipid bilayer.

Biomarkers of Alzheimer's Disease Associated with Programmed Cell Death Reveal Four Repurposed Drugs.

Alzheimer's disease (AD) is a neurodegenerative disorder and the most common cause of dementia. Programmed cell death (PCD) is mainly characterized by unique morphological features and energy-dependent biochemical processes. The predominant pathway leading to cell death in AD has not been thoroughly analyzed, although there is evidence of neuron loss in AD and numerous pathways of PCD have been associated with this process. A better understanding of the systems biology underlying the relationship between AD and PCD could lead to the development of new therapeutic approaches. To this end, publicly available transcriptome data were examined using bioinformatic methods such as differential gene expression and weighted gene coexpression network analysis (WGCNA) to find PCD-related AD biomarkers. The diagnostic significance of these biomarkers was evaluated using a logistic regression-based predictive model. Using these biomarkers, a multifactorial regulatory network was developed. Last, a drug repositioning study was conducted to propose new drugs for the treatment of AD targeting PCD. The development of 3PM (predictive, preventive, and personalized) drugs for the treatment of AD would be enabled by additional research on the effects of these drugs on this disease.

A mathematical model for the role of dopamine-D2 self-regulation in the production of ultradian rhythms.

Many self-motivated and goal-directed behaviours display highly flexible, approximately 4 hour ultradian (shorter than a day) oscillations. Despite lacking direct correspondence to physical cycles in the environment, these ultradian rhythms may be involved in optimizing functional interactions with the environment and reflect intrinsic neural dynamics. Current evidence supports a role of mesostriatal dopamine (DA) in the expression and propagation of ultradian rhythmicity, however, the biochemical processes underpinning these oscillations remain to be identified. Here, we use a mathematical model to investigate D2 autoreceptor-dependent DA self-regulation as the source of ultradian behavioural rhythms. DA concentration at the midbrain-striatal synapses is governed through a dual-negative feedback-loop structure, which naturally gives rise to rhythmicity. This model shows the propensity of striatal DA to produce an ultradian oscillation characterized by a flexible period that is highly sensitive to parameter variations. Circadian (approximately 24 hour) regulation consolidates the ultradian oscillations and alters their response to the phase-dependent, rapid-resetting effect of a transient excitatory stimulus. Within a circadian framework, the ultradian rhythm orchestrates behavioural activity and enhances responsiveness to an external stimulus. This suggests a role for the circadian-ultradian timekeeping hierarchy in governing organized behaviour and shaping daily experience through coordinating the motivation to engage in recurring, albeit not highly predictable events, such as social interactions.

Genome-wide identification, characterization and functional prediction of the SRS gene family in sesame (Sesamum indicum L.)

Sesame (Sesamum indicum L.) is an ancient oilseed crop of the Pedaliaceae family with high oil content and potential health benefits. SHI RELATED SEQUENCE (SRS) proteins are the transcription factors (TFs) specific to plants that contain RING-like zinc figure domain and are associated with the regulation of several physiological and biochemical processes. They also play vital roles in plant growth and development such as root formation, leaf development, floral development, hormone biosynthesis, signal transduction, and biotic and abiotic stress responses. Nevertheless, the SRS gene family was not reported in sesame. In this study, identification, molecular characterization, phylogenetic relationship, cis-acting regulatory elements, protein-protein interaction, syntenic relationship, duplication events and expression pattern of SRS genes were analyzed in S. indicum. We identified total six SiSRS genes on seven different linkage groups in the S. indicum genome by comparing the other species, including the model plant Arabidopsis thaliana. The SiSRS genes showed variation in their structure like 2-5 exons and 1-4 introns. Like other species, SiSRS proteins also contained ‘RING-like zinc figure’ and ‘LRP1’ domains. Then, the SiSRS genes were clustered into subclasses via phylogenetic analysis with proteins of S. indicum, A. thaliana, and some other plant species. The cis-acting regulatory elements analysis revealed that the promoter region of SiSRS4 (SIN_1011561) showed the highest 13 and 16 elements for light- and phytohormone-responses whereas, SiSRS1 (SIN_1015187) showed the highest 15 elements for stress-response. The ABREs, or ABA-responsive elements, were found in a maximum of 8 copies in the SiSRS3 (SIN 1009100). Moreover, the available RNA-seq based expression of SiSRS genes revealed variation in expression patterns between stress-treated and non-treated samples, especially in drought and salinity conditions in. S. indicum. Two SiSRS genes like SiSRS1 (SIN_1015187) and SiSRS5 (SIN_1021065), also exhibited variable expression patterns between control vs PEG-treated sesame root samples and three SiSRS genes, including SiSRS1 (SIN_1015187), SiSRS2 (SIN_1003328) and SiSRS5 (SIN_1021065) were responsive to salinity treatments. The present outcomes will encourage more research into the gene expression and functionality analysis of SiSRS genes in S. indicum and other related species.

Hydrodynamic characterization of bubble column using Dynamical High Order Decomposition approach

Bubble columns play a crucial role in a wide range of industries, including chemical and biochemical processes, petrochemicals, and environmental engineering. Understanding the dynamics of bubble columns is essential for optimizing their performance in various applications. This study proposes a data-driven approach for analyzing the dynamics of a two-dimensional bubble column system. We conducted simulations with varying superficial velocities and generated a comprehensive training dataset encompassing the entire velocity and pressure fields to achieve this. We then compared the performance of two approaches, the Fast Fourier Transformation (FFT) and the High-Order Dynamic Mode Decomposition (HODMD), in representing the system’s dynamics. Our findings demonstrate that the conventional FFT approach fails to adequately capture the complex dynamics of the dispersed multiphase flow system. This limitation arises due to the distribution of frequencies along the domain. Conversely, our work highlights the success of the HODMD method in accurately representing the system’s dynamics using only a few arbitrary sampling points within the domain. The implications of this study are significant, as it sheds light on the potential benefits of employing HODMD for analyzing bubble column dynamics. By utilizing this approach, industrial processes can be optimized more effectively across various applications.