Search results for: trigeminal ganglion cells

Authors: Nancy Awuor Oduor, Nils Moosdorf

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Harmful Algal Blooms (HABs) are a threat to coastal water quality, marine biodiversity, and human health. The attention on HABs and associated phycotoxins is still very low in tropical coastal developing countries despite the high dependence of local communities on coastal and marine resources for food and livelihoods and the growing evidence of the global increase in HABs frequency, toxicity, and geographical expansion. Lack of HABs monitoring thus creates a high risk of exposure due to uncertainty. This study assessed the spatial and temporal variability and effects of potential HAB-forming species in Kenya’s coastal waters. The preliminary results from 463 sampled collected over a series of 10 coastal surveys conducted over 267 Km of Kenya’s coastline between August 2021 and July 2022 revealed the presence of 87 potential algal blooming species belonging to 47 genera dominated by species capable of producing toxins, causing physical harm and high biomass at 41, 31 and 21 % respectively. The taxonomic composition was also dominated by dinoflagellates at 47%, followed by diatoms, cyanobacteria, and silicoflagellates at 39, 12, and 2%, respectively. About 92 % of the toxin-producing species were established in the creek waters. However, there were no significant variations established in species richness between the dry and wet seasons. Paralytic Shellfish Poisoning (PSP) toxin-producing dinoflagellates Alexandrium spp., Aphanizomenon spp., Gonyaulax spp., Gymnodinium spp., and Brachydinium capitatum, and Amnesic Shellfish Poisoning (ASP) Toxin producing diatoms Amphora spp., Nitzschia spp. and Pseudo-nitzschia spp. Frequented the area in low cell densities ranging between 5 and 1500 cells/L. However, no domoic acid (DA) and saxitoxins (SXTs) were detected during the July surveys. This does not mean that the toxins are absent in the area, and longer studies are recommended.

Keywords: harmful algal blooms, phycotoxins, saxitoxin, domoic acid, Kenya

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Authors: Bui Phuong Linh, Yuki Sakakibara, Ryuto Tanaka, Elizabeth H. Pigney, Taishi Hashiguchi

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Non-alcoholic steatohepatitis (NASH) is a chronic liver disease, often associated with type II diabetes, which sometimes progresses to more serious conditions such as liver fibrosis and hepatocellular carcinoma (HCC). NASH has become an important health problem worldwide, buttherapeutic agents for NASH have not yet been approved, and animal models with high clinical correlation are required. TheSTAM™ mouse shows the same pathological progression as human NASH patients and has been widely used for both drug efficacy and basic research, such as lipid profiling and gut microbiota research. In this study, we analyzed the RNA-seq data of STAM™mice at each pathological stage (steatosis, steatohepatitis, liver fibrosis, and HCC) and examined the clinical correlation at the genetic level. NASH was induced in male mice by a single subcutaneous injection of 200 µg streptozotocin solution 2 days after birth and feeding with high fat dietafter 4 weeks of age. The mice were sacrificed and livers collected at 6, 8, 10, 12, 16, and 20 weeks of age. For liver samples, the left lateral lobe was snap frozen in liquid nitrogen and stored at -80˚C for RNA-seq analysis. Total RNA of the cells was isolated using RNeasy mini kit. The gene expression of the canonical pathways in NASH progression from steatosis to hepatocellular carcinoma were analyzed, such as immune system process, oxidation-reduction process, lipid metabolic process. Moreover, since it has been reported that genetic traits are involved in the development of NASH-HCC, we next analyzed the genetic mutations in the STAM™mice. The number of individuals showing mutations in Mtorinvolved in Insulin signaling increases as the disease progresses, especially in the liver cancer phase. These results indicated a clinical correlation of gene profiles in the STAM™mouse.

Keywords: steatosis, non-alcoholic steatohepatitis, fibrosis, hepatocellular carcinoma, RNA-seq

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Authors: Sarmiza Stanca, Wolfgang Fritzsche, Christoph Krafft, Jürgen Popp

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Independent of the cell type a thin layer of a few nanometers thickness surrounds the cell interior as the cellular membrane. The transport of ions and molecules through the membrane is achieved in a very precise way by pores. Understanding the process of opening and closing the pores due to an electrochemical gradient across the membrane requires knowledge of the pore constitutive proteins. Recent reports prove the access to the molecular level of the cellular membrane by atomic force microscopy (AFM). This technique also permits an electrochemical study in the immediate vicinity of the tip. Specific molecules can be electrochemically localized in the natural cellular membrane. Our work aims to recognize the protein domains of the pores using an AFM probe as a miniaturized amperometric sensor, and to follow the protein behavior while changing the applied potential. The intensity of the current produced between the surface and the AFM probe is amplified and detected simultaneously with the surface imaging. The AFM probe plays the role of the working electrode and the substrate, a conductive glass on which the cells are grown, represent the counter electrode. For a better control of the electric potential on the probe, a third electrode Ag/AgCl wire is mounted in the circuit as a reference electrode. The working potential is applied between the electrodes with a programmable source and the current intensity in the circuit is recorded with a multimeter. The applied potential considers the overpotential at the electrode surface and the potential drop due to the current flow through the system. The reported method permits a high resolved electrochemical study of the protein domains on the living cell membrane. The amperometric map identifies areas of different current intensities on the pore depending on the applied potential. The reproducibility of this method is limited by the tip shape, the uncontrollable capacitance, which occurs at the apex and a potential local charge separation.

Keywords: AFM, sensor, membrane, pores, proteins

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Authors: Dileep K. Verma, Sunil K. Lal

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Influenza still remains one of the most challenging diseases posing significant threat to public health causing seasonal epidemics and pandemics. Previous studies suggest that influenza hemagglutinin is essential for viral attachment to host sialic acid receptors and concentrate in lipid rafts for efficient viral fusion. Studies also reported selective nature of Influenza virus to utilize rafts micro-domain for efficient virus assembly and budding. However, the detailed mechanism of Influenza A Virus (IAV) binding to host cell membrane and entry inside the host remains elusive. In the present study, we investigated if host membrane lipid rafts play any significant role in early life cycle events of influenza A virus. Role of host lipid rafts was studied using raft disruption method by extraction of cholesterol and Methyl-β-Cyclodextrin was used to remove membrane cholesterol. We observed co-localization of Influenza A Virus to lipid rafts by visualization of known lipid raft marker GM1 on host cell membrane. Co-localization suggest direct involvement of these micro-domain in initiation of IAV life cycle. We found significant reduction in influenza A virus adsorption in raft disrupted target host cells indicating poor binding and attachment in absence of coherent membrane rafts. Taken together, the results of present study provide evidence for critical involvement of host lipid rafts and its constituents in adsorption process of Influenza A Virus and suggests crucial involvement in other early events of IAV life cycle. The present study opens a new domain to study influenza virus-host interaction and to combat flu at the very early steps of viral life cycle.

Keywords: lipid raft, adsorption, cholesterol, methyl-β-cyclodextrin, GM1

Procedia PDF Downloads 297

Authors: Aliro Villacorta, Laura Rubio, Mohamed Alaraby, Montserrat López Mesas, Victor Fuentes-Cebrian, Oscar H. Moriones, Ricard Marcos, Alba Hernández.

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Micro and nano plastics (MNPLs) are emergent environmental pollutants requiring urgent information on their potential risks to human health. One of the problems associated with the evaluation of their undesirable effects is the lack of real samples matching those resulting from the environmental degradation of plastic wastes. To such end, we propose an easy method to obtain polyethylene terephthalate nano plastics from water plastic bottles (PET-NPLs) but, in principle, applicable to any other plastic goods sources. An extensive characterization indicates that the proposed process produces uniform samples of PET-NPLs of around 100 nm, as determined by using a multi-angle and dynamic light scattering methodology. An important point to be highlighted is that to avoid the metal contamination resulting from methods using metal blades/burrs for milling, trituration, or sanding, we propose to use diamond burrs to produce metal-free samples. To visualize the toxicological profile of the produced PET-NPLs, we have evaluated their ability to be internalized by cells, their cytotoxicity, and their ability to induce oxidative stress and induce DNA damage. In this preliminary approach, we have detected their cellular uptake, but without the induction of significant biological effects. Thus, no relevant increases in toxicity, reactive oxygen species (ROS) induction, or DNA damage -as detected with the comet assay- have been observed. The use of real samples, as produced in this study, will generate relevant data in the discussion about the potential health risks associated with MNPLs exposures.

Keywords: nanoplastics, polyethylene terephthalate, physicochemical characterization, cell uptake, cytotoxicity

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Authors: Shirin jalili, Hadi Shirzad, Mahasti Modarresi, Samaneh Nabavi, Somayeh Khanjani

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Identifying the source tissue of biological material found at crime scenes can be very informative in a number of cases. Despite their usefulness, current visual, catalytic, enzymatic, and immunologic tests for presumptive and confirmatory tissue identification are applicable only to a subset of samples, might suffer limitations such as low specificity, lack of sensitivity, and are substantially impacted by environmental insults. In addition their results are operator-dependent. Recently the possibility of discriminating body fluids using mRNA expression differences in tissues has been described but lack of long term stability of that Molecule and the need to normalize samples for each individual are limiting factors. The use of DNA should solve these issues because of its long term stability and specificity to each body fluid. Cells in the human body have a unique epigenome, which includes differences in DNA methylation in the promoter of genes. DNA methylation, which occurs at the 5′-position of the cytosine in CpG dinucleotides, has great potential for forensic identification of body fluids, because tissue-specific patterns of DNA methylation have been demonstrated, and DNA is less prone to degradation than proteins or RNA. Previous studies have reported several body fluid-specific DNA methylation markers.The presence or absence of a methyl group on the 5’ carbon of the cytosine pyridine ring in CpG dinucleotide regions called ‘CpG islands’ dictates whether the gene is expressed or silenced in the particular body fluid. Were described methylation patterns at tissue specific differentially methylated regions (tDMRs) to be stable and specific, making them excellent markers for tissue identification. The results demonstrate that methylation-based tissue identification is more than a proof-of-concept. The methodology holds promise as another viable forensic DNA analysis tool for characterization of biological materials.

Keywords: DNA methylation, forensic science, epigenome, tDMRs

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Authors: Katarína Čurová, Leonard Siegfried, Radka Vargová, Marta Kmeťová, Vladimír Hrabovský

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Introduction: Cytolethal distending toxins (CDTs) represent intracellular acting proteins which interfere with cell cycle of eukaryotic cells. They are produced by Gram-negative bacteria with afinity to mucocutaneous surfaces and could play a role in the pathogenesis of various diseases. CDTs induce DNA damage probably through DNAse activity, which causes cell cycle arrest and leads to further changes (cell distension and death, apoptosis) depending on the cell type. Five subtypes of CDT (I to V) were reported in E. coli. Methods: We examined 252 E. coli strains belonging to four different groups. Of these strains, 57 were isolated from patients with diarrhea, 65 from patients with urinary tract infections (UTI), 65 from patients with sepsis and 65 from patients with other extraintestinal infections (mostly surgical wounds, decubitus ulcers and respiratory tract infections). Identification of these strains was performed by MALDI-TOF analysis and detection of genes encoding CDTs and determination of the phylogenetic group was performed by PCR. Results: In this study, we detected presence of cdt genes in 11 of 252 E. coli strains tested (4,4 %). Four cdt positive E. coli strains were confirmed in group of UTI (6,15 %), three cdt positive E. coli strains in groups of diarrhea (5,3 %) and other extraintestinal infections (4,6 %). The lowest incidence, one cdt positive E. coli strain, was observed in group of sepsis (1,5 %). All cdt positive E. coli strains belonged to phylogenetic group B2. Conclusion: CDT-producing E. coli are isolated in a low percentage from patients with intestinal and extraintestinal infections, including sepsis and our results correspond with these studies. A weak prevalence of cdt genes suggests that CDTs are not major virulence factors but in combination with other virulence factors may increase virulence potential of E. coli. We suppose that all 11 cdt positive E. coli strains represent real pathogens because they belong to the phylogenetic group B2 which is pathogenic lineage for bacteria E. coli.

Keywords: cytolethal distending toxin, E. coli, phylogenetic group, extraintestinal infection, diarrhea

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Authors: Vongsathorn Ngampuak, Yutachai Chookaew, Wipawee Dejtisakdi

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Dunaliella salina has great potential as a system for generating commercially valuable products, including beta-carotene, pharmaceuticals, and biofuels. Our goal is to improve this potential by enhancing growth rate and other properties of D. salina under optimal growth conditions. We used ethyl methane sulfonate (EMS) to generate random mutants in D. salina KU11, a strain classified in Thailand. In a preliminary experiment, we first treated D. salina cells with 0%, 0.8%, 1.0%, 1.2%, 1.44% and 1.66% EMS to generate a killing curve. After that, we randomly picked 30 candidates from approximately 300 isolated survivor colonies from the 1.44% EMS treatment (which permitted 30% survival) as an initial test of the mutant screen. Among the 30 survivor lines, we found that 2 strains (mutant #17 and #24) had significantly improved growth rates and cell number accumulation at stationary phase approximately up to 1.8 and 1.45 fold, respectively, 2 strains (mutant #6 and #23) had significantly decreased growth rates and cell number accumulation at stationary phase approximately down to 1.4 and 1.35 fold, respectively, while 26 of 30 lines had similar growth rates compared with the wild type control. We also analyzed cell size for each strain and found there was no significant difference comparing all mutants with the wild type. In addition, mutant #24 had shown an increase of biomass accumulation approximately 1.65 fold compared with the wild type strain on day 5 that was entering early stationary phase. From these preliminary results, it could be feasible to identify D. salina mutants with significant improved growth rate, cell accumulation and biomass production compared to the wild type for the further study; this makes it possible to improve this microorganism as a platform for biotechnology application.

Keywords: Dunaliella salina, ethyl methyl sulfonate, growth rate, biomass

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Authors: Rahma Goussi, Walid Derbali, Arafet Manaa, Simone Cantamessa, Graziella Berta, Chedly Abdelly, Roberto Barbato

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Salinity is one of the most important abiotic affecting plant growth and productivity worldwide. Photosynthesis, together with cell growth, is among the primary processes to be affected by salinity. Here, we report the effects of salinity stress on the primary processes of photosynthesis in a model halophyte Thellungiella Salsuginea. Plants were cultivated in hydroponic system with different NaCl concentrations (0, 100, 200 and 400 mM) during 2 weeks. The obtained results showed an obvious change in the photosynthetic efficiency of photosystem I (PSI) and phostosytem II (PSII), related to NaCl concentration supplemented to the medium and the stress duration considered. With moderate salinity (100 and 200 mM NaCl), no significant variation was observed in photosynthetic parameters of PSI and PSII and Chl fluorescence whatever the time of stress application. Also, the photosynthesis apparatus Fo, Fm and Fv fluorescence, as well as Fv/Fm were not affected by salt stress. While a significant decrease was observed on quantum yields Y(I), Y(II) and electron transport rate ETR(I), ETR(II) under high salt treatment (400 mM NaCl) with prolonged period (15 days). This reduction is quantitatively compensated by a corresponding increase of energy dissipation Y(NPQ) and a progressive decrease in Fv/Fm under salt treatment. The intensity of the OJIP fluorescence transient decreased with increase in NaCl concentration, with a major effect observed during prolonged period of salt stress. Ultrastructural analysis with Light Microscopy and Transmission Electron Microscopy of T. salsuginea chloroplasts showed some cellular changes, such as the shape of the mesophyll cells and number of chloroplast/cell only under higher NaCl concentration. Salt-stress caused the swelling of thylakoids in T. Salsuginea mesophyll with more accumulation of starch as compared to control plant.

Keywords: fluorescence, halophyte, photosynthesis, salt stress

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Authors: Rajendra Jangde, Deependra Singh

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Present work was based with objective to release of the antimicrobial and debriding agent in sustained manner at the wound surface. In order to provide a long-lasting antimicrobial action and moist environment on wound space, Biocompatible moist system was developed for complete healing. In the present study, a biocompatible moist system of PVA-gelatin hydrogel was developed capable of carrying multiple drugs- Quercetin and Cabopol in controlled manner for effective and complete wound healing. Carbopol and Quercetin were prepared by thin film hydration techniques and optimized system was incorporated in PVA-Gelatin slurry. PVA-Gelatin hydrogels were prepared by freeze thaw method. The prepared dispersion was casted into films to prepare multiphase hydrogel system and characterized by in vitro and in vivo studies. Results revealed the uniform dispersion of microspheres in a three-dimensional matrix of the PVA-Gelatin hydrogel observed at different magnifications. The in vitro release data showed typical biphasic release pattern, i.e., a burst release followed by a slower sustained release for 5 days. Prepared system was found to be stable under both normal and accelerated conditions. Histopathological study showed significant (p<0.05) increase in fibroblast cells, collagen fibres and blood vessels formation. All parameters such as wound contraction, tensile strength, histopathological and biochemical parameters- hydroxyproline content, protein level, etc. were observed significant (p<0.05) in comparison to control group. Present results suggest an accelerated re-epithelialization under moist wound environment with delivery of multiple drugs effective at different stages of wound healing cascade with minimum disturbance of wound bed.

Keywords: multiphase hydrogel, optimization quercetin, wound healing

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Authors: Azar Sharafianpor, Hossein Rassi, Fahimeh Nemati Mansur

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Cardiovascular diseases (CVD) are the most important cause of death in industrialized and developing countries such as Iran. The most important risk factors for the CVD, genetic factors and chronic infectious agents, such as Helicobacter pylori, can be mentioned. The TNFα gene is one of the most important anti-inflammatory cytokines that can affect the sensitivity, efficacy, and ability of the immune response to chronic infections. Some TNF-α gene polymorphisms, including the replacement of the G nucleotide G with A at position 308 in the promoter region of TNF-α, increase the transcription of cytokines in the target cells and thus predispose a person to chronic infections. This study examines the TNF-α 308 polymorphism and its association with Helicobacter pylori infection in this disease. This study was a case-control study in which 154 patients were examined as cases or patients with symptoms of myocardial infarction or angina and 160 as controls or healthy subjects. All of the subjects at different ages were given venous blood and age, BMI, cholesterol, LDL, and HDL were determined. DNA was extracted from the specimens, and the cagA gene from H. pylori and the TNF-α-308 polymorphism were determined by PCR in patients and healthy subjects. Statistical analysis was performed with Epi Info software. The results showed that the frequency of H. pylori infection in the patients and healthy group were 53.23% (82 out of 154) and 47.5% (76 out of 160). There was no significant difference in H. pylori outbreak between the two groups. The frequencies of TNF-α-308 genotype for GG, GA, and AA in patients were 0.17, 0.49, and 0.34, respectively, whereas for controls 0.47, 0.35, and 0.18 for GG, GA, and AA, respectively. The frequency of genotype analysis of TNF-α-308 polymorphisms in both patients and healthy groups showed that there was a significant difference in the frequency of genotypes and the AA genotype was higher in the affected individuals. Also, there was a significant relationship between the genotype and the contamination with H. pylori and changes in cholesterol, LDL, and HDL levels were observed. The results of the study indicate that H. pylori detection in individuals with AA genotype in people under 50 years of age can play an important role in early diagnosis and treatment of cardiovascular disease.

Keywords: Helicobacter pylori, TNFα gene, cardiovascular diseases, TNFα-308 polymorphism

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Authors: Mohd Aslam Aslam

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Chronic renal failure is a debilitating condition responsible for high morbidity and mortality. Because of its costs and the complexity of its treatment, proper care is available to very few patients in India. According to researchers, the number of adults aged 30 or older who have chronic kidney disease is projected to increase from 13.2 percent currently, to 14.4 percent in 2020 and 16.7 percent in 2030. The aerial part of Aerva lanata (Busehri booti) have been used in kidney disorders by the Unani physicians. In the present study, the effect of extract of Aerva lanata was investigated on cisplatin-induced nephrotoxicity in rats. The renal effects of this drug was evaluated by monitoring levels of blood urea nitrogen (BUN), serum creatinine, serum uric acid in blood and histopathological examination of kidney. Aerva lanata was evaluated at two different doses (1400 mg/kg and 2800 mg/kg). The effect of higher dose was more pronounced in terms of inhibition in the rise of BUN, serum creatinine and uric acid. Higher dose show greater prevention in the rise of BUN, serum creatinine, and uric acid. The histopathological examination of the kidney tissue of the rats treated with aqueous methanolic extract of Aerva lanata (Higher dose-2800 mg/kg) showed marked inhibition of glomerular congestion, tubular casts, peritubular congestion, epithelial desquamation, blood vessel congestion, interstitial edema and inflammatory cells produced by the cisplatin-induced nephrotoxicity. This finding clearly indicates the protective role of Aerva lanata at higher dose. Present investigation validates the use of Aerva lanata in kidney disorders by Unani physicians.

Keywords: Aerva lanata, Busehri booti, nephroprotective, unani medicine

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Authors: Khayra Zerrouki, Noureddine Djebli, Esra Eroglu, Afife Mat, Ozhan Gul

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Neurodegenerative diseases of the human brain comprise a variety of disorders that affect an increasing percentage of the population. Alzheimer’s disease (AD) is a complex, multifactorial, heterogeneous mental illness, which is characterized by an age-dependent loss of memory and an impairment of multiple cognitive functions, but this 10 last years it concerns the population most and most young. Hypericum perforatum has traditionally been used as an external anti-inflammatory and healing remedy for the treatment of swellings, wounds and burns, diseases of the alimentary tract and psychological disorders. It is currently of great interest due to new and important therapeutic applications. In this study, the chemical composition of methanolic extract of Hypericum perforatum (HPM) was analysed by using high performance liquid chromatography – diode array detector (HPLC-DAD). The in vitro antioxidant activity of HPM was evaluated by using several antioxidant tests. HSM exhibits inhibitory capacity against posphatidylcholine liposome peroxidation, induced with iron and ascorbic acid, scavenge DPPH and superoxide radicals and act as reductants. The cytotoxic activity of HSM was also determined by using MTT cell viability assay on HeLa and NRK-52E cell lines. The in vivo activity studies in Swiss mice were determined by using behavioral, memory tests and histological study. According to tests results HPM that may be relevant to the treatment of cognitive disorders. The results of chemical analysis showed a hight level of hyperforin and quercitin that had an important antioxidant activity proved in vitro with the DPPH, anti LPO and SOD; this antioxidant activity was confirmed in vivo after the non-toxic results by means of improvement in behavioral and memory than the reducing shrunken in pyramidal cells of mice brains.

Keywords: AlCl3, alzheimer, mice, neuroprotective, neurotoxicity, phytotherapy

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Authors: Jose Manuel Rodriguez-Dominguez, Rodrigo Barba-Gonzalez, Ernesto Tapia-Campos

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Sprekelia formosissima (L.) Herbert is a bulbous ornamental species of the monocotyledonous Amaryllidaceae family, and it is a perennial, herbaceous monotypic plant commonly known as ‘Aztec Lily’ or ‘Jacobean Lily’; it is distributed through Mexico and Guatemala. Its scarlet flowers with curved petals have made it an exceptional ornamental pot plant. Cytogenetic studies in this species have shown differences in chromosome number (2n=60, 120, 150, 180) with a basic number x=30. Different reports have shown a variable ploidy level (diploid, tetraploid, pentaploid and hexaploid); however, triploid plants have not been reported. In this work, triploid plants of S. formosissima were obtained by crossing tetraploid (2n=4x=120) with diploid (2n=2x=60) genotypes of this species; the seeds obtained from the crosses were placed in pots with a moist substrate made of Peat Moss: Vermiculite (7:3) for germination. Root tips were collected, and metaphasic chromosome preparations were performed. For chromosome counting, the best five metaphases obtained were photographed with a Leica DMRA2 microscope (Leica Microsystems, Germany) microscopy coupled to an Evolution QEI camera under phase contrast (Media-Cybernetics). Chromosomes counting in root-tip cells showed that 100% of the plants were triploid (2n=3x=90). Although tetraploid or pentaploid plants of S. formosissima are highly appreciated, they usually have lower growth rates than related diploid ones. For this reason, it is important to obtain triploid plants, which have advantages such as higher growth rates than tetraploid and pentaploid, larger flowers than those of the diploid plants and they are expected to not be able to produce seeds because their gametes are aneuploids. Furthermore, triploids may become very important for genomic research in the future, creating opportunities for discovering and monitoring genomic and transcriptomic changes in unbalanced genomes, hence the importance of this work.

Keywords: Amaryllidaceae, cytogenetics, ornamental, ploidy level

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Authors: Ozan Kahraman, Hao Feng

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Several models such as Weibull, Modified Gompertz, Biphasic linear, and Log-logistic models have been proposed in order to describe non-linear inactivation kinetics and used to fit non-linear inactivation data of several microorganisms for inactivation by heat, high pressure processing or pulsed electric field. First-order kinetic parameters (D-values and z-values) have often been used in order to identify microbial inactivation by non-thermal processing methods such as ultrasound. Most ultrasonic inactivation studies employed first-order kinetic parameters (D-values and z-values) in order to describe the reduction on microbial survival count. This study was conducted to analyze the E. coli O157:H7 inactivation data by using five microbial survival models (First-order, Weibull, Modified Gompertz, Biphasic linear and Log-logistic). First-order, Weibull, Modified Gompertz, Biphasic linear and Log-logistic kinetic models were used for fitting inactivation curves of Escherichia coli O157:H7. The residual sum of squares and the total sum of squares criteria were used to evaluate the models. The statistical indices of the kinetic models were used to fit inactivation data for E. coli O157:H7 by MTS at three temperatures (40, 50, and 60 0C) and three pressures (100, 200, and 300 kPa). Based on the statistical indices and visual observations, the Weibull and Biphasic models were best fitting of the data for MTS treatment as shown by high R2 values. The non-linear kinetic models, including the Modified Gompertz, First-order, and Log-logistic models did not provide any better fit to data from MTS compared the Weibull and Biphasic models. It was observed that the data found in this study did not follow the first-order kinetics. It is possibly because of the cells which are sensitive to ultrasound treatment were inactivated first, resulting in a fast inactivation period, while those resistant to ultrasound were killed slowly. The Weibull and biphasic models were found as more flexible in order to determine the survival curves of E. coli O157:H7 treated by MTS on apple-carrot juice.

Keywords: Weibull, Biphasic, MTS, kinetic models, E.coli O157:H7

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Authors: Tooba N. Shamsi, Romana Perveen, Sadaf Fatima

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Protease Inhibitors (PIs) are widespread in nature, produced by animals, plants and microorganisms. They play vital role in various biological activities by keeping a check on activity of proteases. Present study aims to investigate antioxidant and anti-inflammatory properties of PPI from Cajanus cajan (CCTI) and Phaseolus limensis (LBTI). PPI was purified from C. cajan (PUSA-992) by ammonium sulfate precipitation followed by ion exchange chromatography. The anti-oxidant activity was analyzed by two most common radical scavenging assays of FRAP (ferric reducing antioxidant power) and DPPH (1,1- diphenyl-2-picrylhydrazyl). Also, in-vitro anti-inflammatory activity was evaluated using albumin denaturation assay and membrane stabilization assay at different concentrations. Ascorbic acid and aspirin were used as a standards for antioxidant and anti-inflammatory assays respectively. The PPIs were also checked for antimicrobial activity against a number of bacterial strains. The CCTI and LBTI showed DPPH radical scavenging activity in a concentration–dependent manner with IC50 values 544 µg/ml and 506 µg/ml respectively comparative to ascorbic acid which was 258 µg/ml. Following FRAP assay, it was evaluated that LBTI had 87.5% and CCTI showed 84.4% antioxidant activity, taking value of standard ascorbic acid to be 100%. The PPIs also showed in-vitro anti‐inflammatory activity by inhibiting the heat induced albumin denaturation with IC50 values of 686 µg/ml and 615 µg/ml for CCTI and LBTI respectively compared to the standard (aspirin) which was 70.8 µg/ml. Red blood cells membrane stabilization with IC50 values of 641 µg/ml and 587 µg/ml for CCTI and LBTI respectively against aspirin which showed IC50 value of 70.4 µg/ml. PPIs showed antibacterial activity against 7 known strains while there was apparently no action against fungi.

Keywords: Cajanus cajan, Phaseolus limensis, Lima beans, protein protease inhibitor, antioxidant, anti-inflammatory, antimicrobial activity

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Authors: Angelis P. Barlampas

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Purpose or Learning Objective It is well known that previous examinations play a major role in futural diagnosis, thus avoiding unnecessary new exams that cost in time and money both for the patient and the health system. A case is presented in which past patient’s results, in combination with the least needed new tests, give an easy final diagnosis. Methods or Background A middle aged man visited the emergency department complaining of hard controlled, persisting fever for the last few days. Laboratory tests showed an elevated number of white blood cells with neutrophil shift and abnormal CRP. The patient was admitted to hospital a month ago for continuing lungs symptomatology after a recent covid-19 infection. Results or Findings Computed tomography scanning showed a solid mass with spiculating margins in right lower lobe. After intravenous iodine contrast administration, there was mildly peripheral enhancement and eccentric non enhancing area. A pneumonic cancer was suspected. Comparison with the patient’s latest computed tomography revealed no mass in the area of interest but only signs of recent post covid-19 lung parenchyma abnormalities. Any new mass that appears in a month’s time span can not be a cancer but a benign lesion. It was obvious that an abscess was the most suitable explanation. The patient was admitted to hospital, and antibiotic therapy was given, with very good results. After a few days, the patient was afebrile and in good condition. Conclusion In this case , a PET scan or a biopsy was avoided, thanks to the patient’s medical history and the availability of previous examinations. It is worthy encouraging the patients to keep their medical records and organizing more efficiently the health system with the current technology of archiving the medical examinations, too.

Keywords: covid-19, chest ct, cancer, abscess, fever

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Authors: Mohammad Moridzadeh, Mohammad Djavid, Barry Doyle

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An assessment of the long-term stability of a cavern in Chagrin shale excavated by the sequential excavation method was performed during and after construction. During the excavation of the cavern, deformations of rock mass were measured at the surface of excavation and within the rock mass by surface and deep measurement instruments. Rock deformations were measured during construction which appeared to result from the as-built excavation sequence that had potentially disturbed the rock and its behavior. Also some additional time dependent rock deformations were observed during and post excavation. Several opinions have been expressed to explain this time dependent deformation including stress changes induced by excavation, strain softening (or creep) in the beddings with and without clay and creep of the shaley rock under compressive stresses. In order to analyze and replicate rock behavior observed during excavation, including current and post excavation elastic, plastic, and time dependent deformation, Finite Element Analysis (FEA) was performed. The analysis was also intended to estimate long term deformation of the rock mass around the excavation. Rock mass behavior including time dependent deformation was measured by means of rock surface convergence points, MPBXs, extended creep testing on the long anchors, and load history data from load cells attached to several long anchors. Direct creep testing of Chagrin Shale was performed on core samples from the wall of the Pump Room. Results of these measurements were used to calibrate the FEA of the excavation. These analyses incorporate time dependent constitutive modeling for the rock to evaluate the potential long term movement in the roof, walls, and invert of the cavern. The modeling was performed due to the concerns regarding the unanticipated behavior of the rock mass as well as the forecast of long term deformation and stability of rock around the excavation.

Keywords: Cavern, Chagrin shale, creep, finite element.

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Authors: Shangqing Song, Bin Xu, Yajun Cheng, Zhong Wang

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miRNAs derived from exosomes exist in a body fluid such as urine were regarded as potential biomarkers for various human cancers diagnosis and prognosis, as mature miRNAs can be steadily preserved by exosomes. However, its potential value in clear cell renal cell carcinoma (ccRCC) diagnosis and prognosis remains unclear. In the present study, differentially expressed miRNAs from urinal exosomes were identified by next-generation sequencing (NGS) technology. The 16 differentially expressed miRNAs were identified between ccRCC patients and healthy donors. To explore the specific diagnosis biomarker of ccRCC, we validated these urinary exosomes from 70 early-stage renal cancer patients, 30 healthy people and other urinary system cancers, including 30 early-stage prostate cancer patients and 30 early-stage bladder cancer patients by qRT-PCR. The results showed that urinary exosome miR-30c-5p could be stably amplified and meanwhile the expression of miR-30c-5p has no significant difference between other urinary system cancers and healthy control, however, expression level of miR-30c-5p in urinary exosomal of ccRCC patients was lower than healthy people and receiver operation characterization (ROC) curve showed that the area under the curve (AUC) values was 0.8192 (95% confidence interval was 0.7388-0.8996, P= 0.0000). In addition, up-regulating miR-30c-5p expression could inhibit renal cell carcinoma cells growth. Lastly, HSP5A was found as a direct target gene of miR-30c-5p. HSP5A depletion reversed the promoting effect of ccRCC growth casued by miR-30c-5p inhibitor, respectively. In conclusion, this study demonstrated that urinary exosomal miR-30c-5p is readily accessible as diagnosis biomarker of early-stage ccRCC, and miR-30c-5p might modulate the expression of HSPA5, which correlated with the progression of ccRCC.

Keywords: clear cell renal cell carcinoma, exosome, HSP5A, miR-30c-5p

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Authors: ZhenlinJu, Christopher P. Vellano, RehanAkbani, Yiling Lu, Gordon B. Mills

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The epithelial–mesenchymal transition (EMT) is a process by which epithelial cells acquire mesenchymal characteristics, such as profound disruption of cell-cell junctions, loss of apical-basolateral polarity, and extensive reorganization of the actin cytoskeleton to induce cell motility and invasion. A hallmark of EMT is its capacity to promote metastasis, which is due in part to activation of several transcription factors and subsequent downregulation of E-cadherin. Unfortunately, current approaches have yet to uncover robust protein marker sets that can classify tumors as possessing strong EMT signatures. In this study, we utilize reverse phase protein array (RPPA) data and consensus clustering methods to successfully classify a subset of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) tumors into an EMT protein signaling group (EMT group). The overall survival (OS) of patients in the EMT group is significantly worse than those in the other Hormone and PI3K/AKT signaling groups. In addition to a shrinkage and selection method for linear regression (LASSO), we applied training/test set and Monte Carlo resampling approaches to identify a set of protein markers that predicts the EMT status of CESC tumors. We fit a logistic model to these protein markers and developed a classifier, which was fixed in the training set and validated in the testing set. The classifier robustly predicted the EMT status of the testing set with an area under the curve (AUC) of 0.975 by Receiver Operating Characteristic (ROC) analysis. This method not only identifies a core set of proteins underlying an EMT signature in cervical cancer patients, but also provides a tool to examine protein predictors that drive molecular subtypes in other diseases.

Keywords: consensus clustering, TCGA CESC, Silhouette, Monte Carlo LASSO

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Authors: Amirhossein Moghanian, Morteza Elsa, Mehrnaz Aminitabar

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Modified bioactive glass has been considered as a promising multifunctional candidate in bone repair and regeneration due to its attractive properties. The present study mainly aims to evaluate how the individual substitution of lithium (L-BG) and magnesium (M-BG) for calcium can affect the in vitro bioactivity of sol-gel derived substituted 58S bioactive glass (BG); and to present one composition in both of the 60SiO2–(36-x)CaO–4P₂O₅–(x)Li₂O and 60SiO₂ –(36-x)CaO–4P₂O₅–(x)MgO quaternary systems (where x= 0, 5, 10 mol.%) with improved biocompatibility, enhanced alkaline phosphatase (ALP) activity, and the most efficient antibacterial activity against methicillin-resistant staphylococcus aureus bacteria. To address these aims, and study the effect of CaO/Li₂O and CaO/MgO substitution up to 10 mol % in 58S-BGs, the samples were characterized by X-ray diffraction, Fourier transform infrared spectroscopy, inductively coupled plasma atomic emission spectrometry and scanning electron microscopy after immersion in simulated body fluid up to 14 days. Results indicated that substitution of either CaO/ Li₂O and CaO/ MgO had a retarding effect on in vitro hydroxyapatite (HA) formation due to the lower supersaturation degree for nucleation of HA compared with 58s-BG. Meanwhile, magnesium had a more pronounced effect. The 3-(4,5dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and alkaline phosphatase (ALP) assays showed that both substitutions of CaO/ Li₂O and CaO/ MgO up to 5mol % in 58s-BGs led to increased biocompatibility and stimulated proliferation of the pre-osteoblast MC3T3 cells with respect to the control. On the other hand, the substitution of either Li or Mg for Ca in the 58s BG composition resulted in improved bactericidal efficiency against MRSA bacteria. Taken together, sample 58s-BG with 5 mol % CaO/Li₂O substitution (BG-5L) was considered as a multifunctional biomaterial in bone repair/regeneration with improved biocompatibility, enhanced ALP activity as well as significant antibacterial activity against methicillin-resistant staphylococcus aureus (MRSA) bacteria.

Keywords: alkaline, alkaline earth, bioactivity, biomedical applications, sol-gel processes

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Authors: A. Kabir, D. Boulainine, I. Bouanane, N. Benslim, B. Boudjema, C. Sedrati

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SnO₂ is an n-type semiconductor with a direct gap of about 3.6 eV. It is largely used in several domains such as nanocrystalline photovoltaic cells. Due to its interesting physic-chemical properties, this material was elaborated in thin film forms using different deposition techniques. It was found that SnO₂ properties were directly affected by the deposition method parameters. In this work, the RGTO method (Rheotaxial Growth and Thermal Oxidation) was used to deposit elaborate SnO₂ thin films. This technique consists on thermal oxidation of the Sn films deposited onto a substrate heated to a temperature close to Sn melting point (232°C). Such process allows the preparation of high porosity tin oxide films which are very suitable for the gas sensing. The films structural, morphological and optical properties pre and post thermal oxidation were studied using X-ray diffraction (XRD), scanning electron microscopy (SEM), UV-Visible spectroscopy and Fourier transform infrared spectroscopy (FTIR) respectively. XRD patterns showed a polycrystalline structure of the cassiterite phase of SnO₂. The grain growth was found affected by the oxidation temperature. This grain size evolution was confronted to existing grain growth models in order to understand the growth mechanism. From SEM images, the as deposited Sn film was formed of difference diameter spherical agglomerations. As a function of the oxidation temperature, these spherical agglomerations shape changed due to the introduction of oxygen ions. The deformed spheres started to interconnect by forming bridges between them. The volume porosity, determined from the UV-Visible reflexion spectra, Changes as a function of the oxidation temperature. The variation of the crystalline fraction, determined from FTIR spectra, correlated with the variation of both the grain size and the volume porosity.

Keywords: tin oxide, RGTO, grain growth, volume porosity, crystalline fraction

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Authors: Juan Alfredo Guevara Carrio, Swamy Toolahalli Thipperudra, Riddhi Naik Dharmeshbhai, Sergio Graniero Echeverrigaray, Jose Vitorio Emiliano, Antonio Helio Castro

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In order to advance the hydrogen economy, several industrial sectors can potentially benefit from the trillions of stimulus spending for post-coronavirus. Blending hydrogen into natural gas pipeline networks has been proposed as a means of delivering it during the early market development phase, using separation and purification technologies downstream to extract the pure H₂ close to the point of end-use. This first step has been mentioned around the world as an opportunity to use existing infrastructures for immediate decarbonisation pathways. Among current technologies used to extract hydrogen from mixtures in pipelines or liquid carriers, membrane separation can achieve the highest selectivity. The most efficient approach for the separation of H₂ from other substances by membranes is offered from the research of 2D layered materials due to their exceptional physical and chemical properties. Graphene-based membranes, with their distribution of pore sizes in nanometers and angstrom range, have shown fundamental and economic advantages over other materials. Their combination with the structure of ceramic and geopolymeric materials enabled the synthesis of nanocomposites and the fabrication of membranes with long-term stability and robustness in a relevant range of physical and chemical conditions. Versatile separation modules have been developed for hydrogen separation, which adaptability allows their integration in industrial prototypes for applications in heavy transport, steel, and cement production, as well as small installations at end-user stations of pipeline networks. The developed membranes and prototypes are a practical contribution to the technological challenge of supply pure H₂ for the mentioned industries as well as hydrogen energy-based fuel cells.

Keywords: graphene nano-composite membranes, hydrogen separation and purification, separation modules, indsutrial prototype

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Authors: Muhammad Zainuddin Arriafdi, Hamudah Hakimah Abdullah, Mohd Helmi Sani, Wan Azlina Ahmad, Muhd Nazrul Hisham Zainal Alam

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The biotechnology process development demands numerous experimental works. In laboratory environment, this is typically carried out using a shake flask platform. This paper presents the design and fabrication of a miniature bioreactor system as an alternative research tool for bioprocessing. The working volume of the reactor is 100 ml, and it is made of plastic. The main features of the reactor included stirring control, temperature control via the electrical heater, aeration strategy through a miniature air compressor, and online optical cell density (OD) sensing. All sensors and actuators integrated into the reactor was controlled using an Arduino microcontroller platform. In order to demonstrate the functionality of such miniature bioreactor concept, series of batch Saccharomyces cerevisiae fermentation experiments were performed under various glucose concentrations. Results attained from the fermentation experiments were utilized to solve the Monod equation constants, namely the saturation constant, Ks, and cells maximum growth rate, μmax as to further highlight the usefulness of the device. The mixing capacity of the reactor was also evaluated. It was found that the results attained from the miniature bioreactor prototype were comparable to results achieved using a shake flask. The unique features of the device as compared to shake flask platform is that the reactor mixing condition is much more comparable to a lab-scale bioreactor setup. The prototype is also integrated with an online OD sensor, and as such, no sampling was needed to monitor the progress of the reaction performed. Operating cost and medium consumption are also low and thus, making it much more economical to be utilized for biotechnology process development compared to lab-scale bioreactors.

Keywords: biotechnology, miniature bioreactor, research tools, Saccharomyces cerevisiae

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Authors: Fendouli Ines, Zaafrane Nesrine, Mhamdi Hana, Knani Leila, Ghorbel Mohamed

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Introduction: Ocular infiltration of leukemia can involve orbit, uveal tract, retina and optic nerve. It may result from direct ocular infiltration by leukemic cells or indirect ocular involvement resulting from secondary hematologic changes, opportunistic infections and complications of various modalities of therapy. We here in report a case of central venous retinal occlusion associated to optic nerve infiltration as presenting signs of a relapse of acute lymphoblastic leukemia. Case Report: A twelve-year-old male -patient of acute B lymphoblastic leukemia presented with headaches and bilateral blurred vision in the left ee. Ophthalmic examination showed a visual acuity reduced to counting fingers in the right eye and no light perception in the left eye. Funduscopy revealed a voluminous disc edema surrounded by retinal haemorrhages in the right eye, and venous tortusities, papillary edema, and hemorrages suggesting central retinal venous occlusion in the LE. Swept source optical coherence tomography revealed a serous retinal detachment in the RE and .hyperreflective inner layers with macular edema in the left eye. Cerebro-orbital MRI showed bilateral thickened left optic nerve. There were no radiological signs of true papillary edema due to intracranial hypertension secondary to central nervous system involvement. Myelogram and lumbar punction demonstrated blast infiltration and confirmed ocular relapse of the leukemia. Conclusion: Ocular involvement lymphoblastic acute leukemias decreased since the introduction of a systematic prophylactic treatment of central nervous system. Periodic ophthalmic examination is necessary to allow early diagnosis and treatment.

Keywords: acute leukemia, optic nerve, infiltration, relapse

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Authors: Q. Giraud, J. Gonçalvès, B. Paris

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Remediation of dense non-aqueous phase liquids (DNAPLs) represents a challenging issue because of their persistent behaviour in the environment. This pilot-scale study investigates, by means of in situ experiments and numerical modelling, the feasibility of the pulsed pumping process of a large amount of a DNAPL in an alluvial aquifer. The main compound of the DNAPL is hexachlorobutadiene, an emerging organic pollutant. A low-permeability keyed enclosure was built at the location of the DNAPL source zone in order to isolate a finite undisturbed volume of soil, and a 3-month pulsed pumping process was applied inside the enclosure to exclusively extract the DNAPL. The water/DNAPL interface elevation at both the pumping and observation wells and the cumulated pumped volume of DNAPL were also recorded. A total volume of about 20m³ of purely DNAPL was recovered since no water was extracted during the process. The three-dimensional and multiphase flow simulator TMVOC was used, and a conceptual model was elaborated and generated with the pre/post-processing tool mView. Numerical model consisted of 10 layers of variable thickness and 5060 grid cells. Numerical simulations reproduce the pulsed pumping process and show an excellent match between simulated, and field data of DNAPL cumulated pumped volume and a reasonable agreement between modelled and observed data for the evolution of the water/DNAPL interface elevations at the two wells. This study offers a new perspective in remediation since DNAPL pumping system optimisation may be performed where a large amount of DNAPL is encountered.

Keywords: dense non-aqueous phase liquid (DNAPL), hexachlorobutadiene, in situ pulsed pumping, multiphase flow, numerical modelling, porous media

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Authors: Kairat Uteulin, Azhar Iskakova, Serik Mukhambetzhanov, Bayan Yesbolayeva, Gabit Bari, Aslan Zheksenbai, Kabyl Zhambakin, Chingis Dzhabykbayev, Vladimir Piven, Izbasar Rakhimbaiev

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To explore the potential for in vitro rapid regeneration of Russian dandelion (Taraxacum kok-saghyz Rodin), different concentrations of 6-Benzylaminopurine (BAP), 2,4-Dichlorophenoxyacetic acid (2.4-D) and BAP combined with Indole-3-acetic acid (IAA) were evaluated for their effects on the induction of somatic embryos from leaf, seed stem and root explants. Different explants were cultured on MS medium supplemented with various concentrations (0, 0.5, 1, 1.5, 2, 2.5 and 3 mg/l) of each kind of hormone. Callus induction percentage, fresh weight, color and texture of the callus were assessed after 14 and 28 days of culture. The optimum medium for the proliferation of embryogenic calli from leaf and root explants was MS supplemented with 2.5 mg/L BAP and 0.5 mg/L 2.4-D. Concentrations of 2.5 mg/L BAP and 1.5 mg/L IAA also had a remarkable effect on root and stem explants. The best concentration to produce callus from stem explants was 0.5 mg/L BAP and 1 mg/L IAA. Results of mean comparison showed that BAP and 2.4-D were more effective on different explants than BAP and IAA. Results of the double staining method proved that somatic embryogenesis occurred in the most concentrations of BAP and 2.4-D. Under microscopic observations, the different developmental stages of the embryos (globular, heart, torpedo and cotyledonary) were revealed together in callus cells, indicating that the most tested hormone combinations were effective for somatic embryogenesis formation in this species. Seed explants formed torpedo and cotyledonary stages faster than leaf and root explants in the most combinations. Most calli from seed explants were cream colored and friable, while calli were compact and light green from leaf and root explants. Some combinations gave direct regeneration and (3 mg/L BAP and 2 mg/L IAA) in seed explants and (0.5 mg/L BAP and 2.5 mg/L IAA) in leaf explants had the highest number of shoots with average of 21 and 27 shoots per callus. The developed protocol established the production of different callus types from seed, leaf, and root explants and plant regeneration through somatic embryogenesis.

Keywords: taraxacum kok-saghyz Rodin, callus, somatic embryogenesis

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Authors: Sani Ismaila, Shafiu Yau, Abubakar Salisu, Buhari Salisu, Sharifat Balogun, Mustapha Abubakar, Biobaku Khalid, Agaie Bello

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Over the years, Japanese quail egg has been in use in the management of diseases. The objective of this study was to evaluate the analgesic, anti-inflammatory and gastroprotective effects of raw Quail egg (yolk + albumin) in rats. Pain was assessed in rats by recording the latent period and writing reflex, anti-inflammatory effect was determined using both motility and compression test, while the gastro-protective effects were assessed by observing the histology of the stomach after diclofenac-induced gastric ulcers and subsequent treatment with the quail egg, Rats were randomly assigned into 4 groups; Groups I: were the control non-treated (NT), Group II were treated with Tramadol 50 mg/kg/Os (TMD) or Indomethacin (IND) 5mg/kg/Os (positive control for the writhing reflex determination), while group III and IV were treated with 3 and 6g/kg of raw quail egg respectively). Groups treated with quail egg in both doses showed a significant increase in the latent period (p <0 .05) when compared to the control NT, but lower than the group treated with tramadol at 20mins interval (p<0.05). Writing reflexes decrease in groups II, III, and IV compared to the NT group (p < 0.05). While motility increases significantly (p < 0.05) in groups II, compared to I (p<0.05). Control non-treated rats showed a quicker and extensive response to compression using the Vanier calliper on the inflamed paw compared to groups II-IV (p < 0.05). Histological studies of the stomach revealed sloughing of the epithelia, cellular infiltration with micro abscesses in the non-treated, while groups treated concurrently with quail egg showed proliferation of the glandular epithelia and goblet cells, and those treated 30 minutes before diclofenac administration showed proliferation of glands and thickening of the squamous epithelia. This study showed that quail egg has analgesic, anti-inflammatory and gastro-protective potentials and can be used as adjuvant treatment whenever COX-2 enzymes inhibitors are indicated.

Keywords: analgesia, anti-inflammatory, gastroprotective effect, japanese quail egg

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Authors: Yong Chen

Abstract:

To understand the detailed molecular mechanisms of memory formation in engram cells is one of the most fundamental questions in neuroscience. Recent single-cell RNA-seq (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) techniques have allowed us to explore the sparsely activated engram ensembles, enabling access to the molecular mechanisms that underlie experience-dependent memory formation and consolidation. However, the absence of specific and powerful computational methods to detect memory-related genes (modules) and their regulatory relationships in the sc/snRNA-seq datasets has strictly limited the analysis of underlying mechanisms and memory coding principles in mammalian brains. Here, we present a deep-learning method named SCENTBOX, to detect memory-related gene modules and causal regulatory relationships among themfromsc/snRNA-seq datasets. SCENTBOX first constructs codifferential expression gene network (CEGN) from case versus control sc/snRNA-seq datasets. It then detects the highly correlated modules of differential expression genes (DEGs) in CEGN. The deep network embedding and attention-based convolutional neural network strategies are employed to precisely detect regulatory relationships among DEG genes in a module. We applied them on scRNA-seq datasets of TRAP; Ai14 mouse neurons with fear memory and detected not only known memory-related genes, but also the modules and potential causal regulations. Our results provided novel regulations within an interesting module, including Arc, Bdnf, Creb, Dusp1, Rgs4, and Btg2. Overall, our methods provide a general computational tool for processing sc/snRNA-seq data from case versus control studie and a systematic investigation of fear-memory-related gene modules.

Keywords: sc/snRNA-seq, memory formation, deep learning, gene module, causal inference

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Authors: Marianna Ciaccia, Gennaro Agrimi, Isabella Pisano, Maurizio Bettiga, Silvia Rapacioli, Giulia Mensa, Monica Marzagalli

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Objective: Untargeted metabolomic analysis of extracellular metabolites is a powerful approach that focuses on comprehensively profiling in the extracellular space. In this study, we applied extracellular metabolomic analysis to investigate the metabolism of two probiotic microorganisms with health benefits that extend far beyond the digestive tract and the immune system. Methods: Analytical techniques employed in extracellular metabolomic analysis encompass various technologies, including mass spectrometry (MS), which enables the identification of metabolites present in the fermentation media, as well as the comparison of metabolic profiles under different experimental conditions. Multivariate statistical analysis techniques like principal component analysis (PCA) or partial least squares-discriminant analysis (PLS-DA) play a crucial role in uncovering metabolic signatures and understanding the dynamics of metabolic networks. Results: Different types of supernatants from fermentation processes, such as dairy-free, not dairy-free media and media with no cells or pasteurized, were subjected to metabolite profiling, which contained a complex mixture of metabolites, including substrates, intermediates, and end-products. This profiling provided insights into the metabolic activity of the microorganisms. The integration of advanced software tools has facilitated the identification and characterization of metabolites in different fermentation conditions and microorganism strains. Conclusions: In conclusion, untargeted extracellular metabolomic analysis, combined with software tools, allowed the study of the metabolites consumed and produced during the fermentation processes of probiotic microorganisms. Ongoing advancements in data analysis methods will further enhance the application of extracellular metabolomic analysis in fermentation research, leading to improved bioproduction and the advancement of sustainable manufacturing processes.

Keywords: biotechnology, metabolomics, lactic bacteria, probiotics, postbiotics

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