Growth Medium Research Articles

Respons Fisiologis Bibit Kopi Robusta dalam Kondisi Cekaman Kekeringan terhadap Aplikasi Trichoderma spp. Cair

Abiotic stresses caused by climate change can affect on the growth of coffee trees. The application of liquid Trichoderma spp. might stimulate growth and enhance plant defense mechanisms in suboptimal conditions. The purpose of this study was to Evaluating the physiological responses of Robusta coffee seedlings BP 939 and BP 308 and obtaining Robusta coffee seedlings that produce the best physiological responses under drought stress conditions against Trichoderma spp. applications in liquid medium. The experiment was carried out using a Randomized Group Design (RAG) with 8 treatments repeated 4 times, namely : coffea clone BP 939 control; coffea clone BP 308 control.; coffea clone BP 939 Trichoderma spp.; coffea clone BP 308 Trichoderma spp.; coffea clone BP 939 with drought; coffea clone BP 308 with drought; coffea clone BP 939 with drought + Trichoderma spp.; coffea clone BP 308 with drought + Trichoderma spp. The experiment results show that the application of Trichoderma spp. in liquid medium does not exhibit significant physiological responses, and the Robusta coffee seedlings of clones BP 939 and BP 308 show the same effect under drought stress conditions. However, the Robusta coffee clone BP 308 treated with Trichoderma spp. showed significant physiological responses at 12 hours after treatment.

Production and Antimicrobial Activities of Pyocyanin Extracts from Pseudomonas aeruginosa

Pyocyanin is a blue-green phenazine pigment synthesized by Pseudomonas aeruginosa that has significant biotechnological applications. The present study aims to investigate pyocyanin extracts of multi-drug resistant P. aeruginosa isolates sourced from hospital wastewater and evaluate their antimicrobial activity against a panel of clinically relevant pathogens such as Staphylococcus aureus, Salmonella typhi, Achromobacter xylosoxidans and Candida albicans. Nutrient broth and King’s A broth supplemented with 1% nutrient supplements such as rice water and groundnut cake powder were used as a production medium. Extracted pyocyanin was confirmed by FTIR analysis. The isolates P8 and P9 demonstrated of varying concentrations of pyocyanin in different media. Isolate P8 showed maximum pyocyanin production in King’s A broth compared to nutrient broth with pyocyanin yields 14.34 (µg/mL) and 5.63 (µg/mL), respectively, without the nutrient supplements. Preliminary antimicrobial activity of the pyocyanin extracts exhibited substantial inhibition of tested bacterial culture at a concentration of 25 mg/µl; however, did not show any antifungal activity against tested fungi.

First report on the physicochemical and proteomic characterization of Proteus mirabilis outer membrane vesicles under urine-mimicking growth conditions: comparative analysis with Escherichia coli

IntroductionUropathogenic bacteria employ multiple strategies to colonize the urinary tract, including biofilm formation, invasion of urothelial cells, and the production of adhesins, toxins, and siderophores. Among the most prevalent pathogens causing urinary tract infections (UTIs) are Uropathogenic Escherichia coli and Proteus mirabilis. A notable feature of Gram-negative bacteria is their ability to produce outer membrane vesicles (OMVs), which play critical roles in bacterial survival, virulence, and host-pathogen interactions, including UTIs.MethodsIn this study, OMVs were isolated and characterized from two clinical strains, E. coli U144 and P. mirabilis 2,921, cultured in both Luria-Bertani broth and artificial urine.Result and discussionThe OMVs ranged in size from 85 to 260 nm, with the largest vesicles observed in artificial urine. Proteomic analysis allowed the identification of 282 proteins in OMVs from E. coli and 353 proteins from P. mirabilis when cultured LB medium, while 215 were identified from E. coli and 103 from P. mirabilis when cultured in artificial urine. The majority of these proteins originated from the bacterial envelope, while others were linked to motility and adhesion. Notably, the protein composition of OMVs varied depending on the growth medium, and proteins associated with zinc and iron uptake being more prominent in artificial urine, suggesting their importance in the urinary environment. Crucially, this is the first report to characterize P. mirabilis OMVs under different culture conditions, offering novel insights into the role of OMVs in UTI pathogenesis. These findings provide a deeper understanding of the molecular mechanisms by which OMVs contribute to bacterial virulence, establishing the foundation for potential therapeutic interventions targeting OMV-mediated processes in UTIs.

Genome-wide comparative analysis of clinical and environmental strains of the opportunistic pathogen Paracoccus yeei (Alphaproteobacteria)

IntroductionParacoccus yeei is the first species in the genus Paracoccus to be implicated in opportunistic infections in humans. As a result, P. yeei strains provide a valuable model for exploring how bacteria shift from a saprophytic to a pathogenic lifestyle, as well as for investigating the role of horizontally transferred DNA in this transition. In order to gain deeper insights into the unique characteristics of this bacterium and the molecular mechanisms underlying its opportunistic behavior, a comparative physiological and genomic analysis of P. yeei strains was performed.ResultsComplete genomic sequences of 7 P. yeei isolates (both clinical and environmental) were obtained and analyzed. All genomes have a multipartite structure comprising numerous extrachromosomal replicons (59 different ECRs in total), including large chromids of the DnaA-like and RepB families. Within the mobile part of the P. yeei genomes (ECRs and transposable elements, TEs), a novel non-autonomous MITE-type element was identified. Detailed genus-wide comparative genomic analysis permitted the identification of P. yeei-specific genes, including several putative virulence determinants. One of these, the URE gene cluster, determines the ureolytic activity of P. yeei strains—a unique feature among Paracoccus spp. This activity is induced by the inclusion of urea in the growth medium and is dependent on the presence of an intact nikR regulatory gene, which presumably regulates expression of nickel (urease cofactor) transporter genes.DiscussionThis in-depth comparative analysis provides a detailed insight into the structure, composition and properties of P. yeei genomes. Several predicted virulence determinants (including URE gene clusters) were identified within ECRs, indicating an important role for the flexible genome in determining the opportunistic properties of this bacterium.

Pengaruh Penambahan Minyak Nabati pada Media Tumbuh terhadap Pertumbuhan Cendawan Entomopatogen Lecanicillium lecanii

Pest attacks are one of the challenges frequently encountered in rice cultivation. Effective and environmentally friendly control can be achieved with the entomopathogenic fungus Lecanicillium lecanii. The addition of vegetable oils such as peanut oil and castor oil can enhance the growth and development of the entomopathogenic fungus. This study aims to find the corn growth medium with the addition of vegetable oils that provides the best effect for the growth of the entomopathogenic fungus L. lecanii. The method used is a Completely Randomized Design (CRD) with a single factor consisting of 7 treatments with 4 replications: Control (Corn Medium); T1 (Corn + Peanut Oil 2 ml); T2 (Corn + Peanut Oil 5 ml); T3 (Corn + Peanut Oil 10 ml); J1 (Corn + Castor Oil 2 ml); J2 (Corn + Castor Oil 5 ml); J3 (Corn + Castor Oil 10 ml). The results of this study indicate that the addition of vegetable oils to the corn growth medium has a significant effect on the growth of the entomopathogenic fungus L. lecanii. The most effective growth medium for L. lecanii is corn medium + 10 ml peanut oil, providing an incubation period of 1 days and a colony diameter of 8.00 cm.

A functional dual responsive CMC/OHA/SA/TOB hydrogel as wound dressing to enhance wound healing.

Within the clinical realm, the complexities of wound healing have consistently presented formidable challenges. Recent advancements, notably in hydrogel technologies, have broadened the therapeutic spectrum. This study focuses on investigating a novel dual responsive composite hydrogel for wound healing. This hydrogel is ingeniously designed to maintain an optimal moist environment, expedite healing, and combat bacterial infection during wound recovery. This study combining carboxymethyl chitosan (CMC), oxidized hyaluronic acid (OHA), and sodium alginate (SA), in addition, tobramycin (TOB) was incorporated to create a CMC/OHA/SA/TOB hydrogel. Hydrogel cross-linking was verified by infrared spectroscopy, and the microstructure was examined with scanning electron microscopy. We explored its swelling and degradation behaviors in different pH environments. The drug release profile and biocompatibility was evaluated via cytotoxicity and hemolysis assays. The antibacterial efficacy of hydrogel was tested in both solid and liquid media. Additionally, the wound models in Sprague-Dawley (SD) rat was employed to investigate the hydrogel's wound healing capabilities in vivo. Results showed that CMCOHA/SA/TOB hydrogel was effectively cross-linked with a network structure. The hydrogel exhibited pronounced responsiveness in its swelling and degradation characteristics, which was significantly influenced by different levels of pH. In vitro results demonstrated that the CMC/OHA/SA/TOB hydrogel exhibits limited cytotoxicity and hemolysis, coupled with a drug release profile of dual responsive characteristics. Antibacterial activity of the hydrogel against Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli was confirmed. Furthermore, in vivo experiments underscored the hydrogel's proficiency in promoting wound healing, highlighting its potential for clinical applications. The CMC/OHA/SA/TOB hydrogel not only fosters a moist environment essential for wound healing and enhances structural stability, but it also exhibits functional dual responsive capabilities in swelling and degradation. These distinctive abilities enable the precise release of TOB, thereby optimizing wound healing.

Exploring the lipids, carotenoids, and vitamins content of Rhodotorula glutinis with selenium supplementation under lipid accumulating and growth proliferation conditions.

Rhodotorula glutinis, a specific type of yeast, has been recognised as a superior resource for generating selenium-enriched biomass that possesses exceptional nutritional and functional attributes. The purpose of this investigation was to assess the effect of sodium selenite at different concentrations on lipid and carotenoid synthesis, as well as the growth of R. glutinis. The lipid's fatty acid composition was determined using gas chromatography (GC). The vitamins were detected by high-performance liquid chromatography (HPLC). Transmission electron microscopy was used to detect the structural modification of yeast cells caused by the addition of sodium selenite to the growth medium, as well as the accumulation of elemental selenium in the yeast cells. The yeast cells demonstrated the ability to endure high concentrations of sodium selenite under lipid accumulation (LAM) and growth-promoting (YPD) conditions. 25.0 mM and 30.0 mM, respectively, were published as the IC50 values for the LAM and YPD conditions. In both growth media, 1 mM sodium selenite boosted lipid synthesis. Lipid accumulation increased 26% in LAM to 11.4g/l and 18% in YPD to 4.3g/l. Adding 1 mM and 3 mM sodium selenite to YPD medium increased total and cellular carotenoids by 22.8% (646.7µg/L and 32.12µg/g) and 48.7% (783.3µg/L and 36.43µg/g), respectively. Palmitic acid was identified as the most abundant fatty acid in all treatments, followed by oleic acid and linoleic acid. The concentrations of water soluble vitamins (WSV) and fat soluble vitamins (FSV) were generally significantly increased after supplementation with 1.0 mM sodium selenite. TEM examination revealed a significant reduction in lipid bodies accumulation in the yeast cells when sodium selenite was added to lipid-promoting environments. This decline is accompanied by an augmentation in the formation of peroxisomes, indicating that selenium has a direct impact on the degradation of fatty acids. In addition, autophagy appears to be the primary mechanism by which selenium ions are detoxified. Additionally, intracellular organelles disintegrate, cytoplasmic vacuolization occurs, and the cell wall and plasma membrane rupture, resulting in the discharge of cytoplasmic contents, when a high concentration of sodium selenite (20.0 mM) is added. Also, the presence of numerous electron-dense granules suggests an intracellular selenium-detoxification pathway. This study proposes the use of YPD with 1 mM sodium selenite to cultivate selenium-enriched biomass from R. glutinis. This approach leads to heightened lipid levels with higher accumulation of oleic, linoleic and linolenic acids, carotenoids, and vitamins. Hence, this biomass has the potential to be a valuable additive for animal, fish, and poultry feed. Furthermore, explain certain potential factors that indicate the impact of selenium in reducing the accumulation of lipid droplets in R. glutinis during lipogenesis, as detected through TEM examination.

A New Approach to Evaluate the Bactericidal Activity of Different Antiseptic Ophthalmic Preparations Used as Surgical Prophylaxis

Background: A survey conducted by the European Observatory on Cataract Surgery showed high heterogeneity in the use of antiseptics both preoperatively and in the operating room, highlighting the absence of a global consensus regarding ocular infection prophylaxis in cataract surgery. Methods: The antibacterial activity of seven antiseptic ophthalmic formulations (AOFs) registered as medical devices and the two most common disinfectants were evaluated in vitro against five bacterial species. The viability of bacterial strains after exposure to the antiseptic was evaluated with different techniques: the in vitro Minimum Inhibitory Concentration and the subsequent Minimum Bactericidal Concentration, performed on liquid and solid culture medium. Furthermore, a real-time assessment of bacterial viability was conducted using double staining for live/dead bacterial cells by fluorimetric assay. This evaluation was performed on both the time-killing curve and the tear dilution effect test. Results: We observed a high variability across the different AOFs in terms of inhibitory/bactericidal concentration and timing on Gram-positive and Gram-negative bacterial classes. The results indicated that among the tested AOFs, Visuprime, Iodim, and Oftasteril were the most rapid and effective for ocular surface disinfection against the tested bacterial species. Conclusions: The obtained results can support the clinician’s choice of the most suitable AOF for the prevention and treatment of ophthalmic infections associated with surgery.

Establishment of a human 3D in vitro liver-bone model as a potential system for drug toxicity screening.

Drug toxicity is an important cause of chronic liver damage, which in the long term can lead to impaired bone homeostasis through an imbalance in the liver-bone axis. For instance, non-steroidal anti-inflammatory drugs (e.g., diclofenac), which are commonly used to control pain during orthopaedic interventions, are known to reduce bone quality and are the most prevalent causes of drug-induced liver damage. Therefore, we used human cell lines to produce a stable, reproducible, and reliable in vitro liver-bone co-culture model, which mimics the impaired bone homeostasis seen after diclofenac intake in vivo. To provide the best cell culture conditions for the two systems, we tested the effects of supplements contained in liver and bone cell culture medium on liver and bone cell lines, respectively. Additionally, different ratios of culture medium combinations on bone cell scaffolds and liver spheroids' viability and function were also analysed. Then, liver spheroids and bone scaffolds were daily exposed to 3-6µM diclofenac alone or in co-culture to compare and evaluate its effect on the liver and bone system. Our results demonstrated that a 50:50 liver:bone medium combination maintains the function of liver spheroids and bone scaffolds for up to 21days. Osteoclast-like cell activity was significantly upregulated after chronic exposure to diclofenac only in bone scaffolds co-cultured with liver spheroids. Consequently, the mineral content and stiffness of bone scaffolds treated with diclofenac in co-culture with liver spheroids were significantly reduced. Interestingly, our results show that the increase in osteoclastic activity in the system is not related to the main product of diclofenac metabolism. However, osteoclast activation correlated with the increase in oxidative stress and inflammation associated with chronic diclofenac exposure. In summary, we established a long-term stable liver-bone system that represents the interaction between the two organs, meanwhile, it is also an outstanding model for studying the toxicity of drugs on bone homeostasis.

Diversity of Oomycetes From Alabama Cotton Soils Using Culture-Independent Methods.

Seedling disease management recommendations rely on comprehensive identification of the pathogens. A recent manuscript isolated oomycetes from diseased cotton (Gossypium hirsutum L.) roots to identify the species associated. However, culture-dependent surveys may miss species because of the microbiological medium and work required to isolate and maintain all cultured organisms. Alternatively, culture-independent methods using PCR amplification and high-throughput sequencing can identify species' presence and relative abundance, including obligate pathogens and rare members of communities. We used culture-independent sequencing from the same cotton soils in the culture-based survey to determine the oomycete species in oomycete-containing soils. The results of the two methods were generally similar regarding the species identified. Similarly to the culture-based method, Globisporangium irregular accounted for 24% of the relative abundance and was encountered in all fields sequenced. In contrast, we identified three operational taxonomic units matching Globisporangium ultimum, but accounted for less than 0.06% of total relative abundance, potentially explaining why it was not isolated from cotton roots in the original survey. Phytophthora nicotianae was identified in soils but not at the concentrations recorded in the culture-based study. The results of this study, combined with the results of the culture-based survey, demonstrate the most comprehensive identification of oomycetes associated with cotton in the cotton belt and the oomycetes related to seedling disease. The combined results will be essential for future research into the specific pathogen species mentioned and stimulate similar research in other states.

Modifications of the respiratory chain of Bacillus licheniformis as an alkalophilic and cyanide-degrading microorganism.

Bacillus licheniformis can use cyanide as a nitrogen source for its growth. However, it can also carry out aerobic respiration in the presence of this compound, a classic inhibitor of mammalian cytochrome c oxidase, indicating that B. licheniformis has a branched respiratory chain with various terminal oxidases. Here, we studied the modifications in the respiratory chain of B. licheniformis when cells were cultured in Nutrient Broth, an alkaline medium with ammonium, or an alkaline medium with cyanide. Then, we measured oxygen consumption in intact cells and membranes, enzyme activities, carried out 1D and 2D-BN-PAGE, followed by mass spectrometry analysis of BN-PAGE bands associated with NADH, NADPH, and succinate dehydrogenase activities. We found that cell growth was favored in a nutrient medium than in an alkaline medium with cyanide. In parallel, respiratory activity progressively decreased in cells cultured in the rich medium, alkaline medium with ammonium, and the lowest activity was in the cells growing in the alkaline medium with cyanide. B. licheniformis membranes contain NADH, NADPH, and succinate dehydrogenases, and the proteomic analysis detected the nitrate reductase and the bc, caa3, aa3, and bd complexes. The succinate dehydrogenase migrated with a molecular mass of 375kDa, indicating its association with the nitrate reductase (115kDa + 241kDa, respectively). The NADH dehydrogenase of B. licheniformis forms aggregates of different molecular mass.

Establishment of 3D Cultures of Myometrium, Leiomyoma, and Leiomyosarcoma Cells: Advantages and Disadvantages of Two Different Models.

Uterine leiomyomas are the most common benign, monoclonal, gynaecological tumors in a woman's uterus, while leiomyosarcoma is a rare but aggressive condition caused by the malignant transformation of the myometrium. To overcome the common obstacles related to the methods usually used to study these pathologies, we aimed to devise three-dimensional models of myometrium, uterine leiomyoma and leiomyosarcoma cell lines, using two different types of biocompatible scaffolds. Specifically, we exploited the agarose gel matrix in common 6-well plates and the alginate matrix using Bioprinting INKREDIBLE + (CELLINK), a pneumatic extruded base equipped with a system with double printheads, and a UV printer LED curing system. Both methods allowed the development of 3D spheroids of all three cell types, that were also suitable for morphological investigations. We showed that all cell types embedded in both agarose and alginate formed spheroids in their growth medium. The spheroids successfully proliferated and self-organized into complex structures, developing a sustainable system that emulated the condition of the tissues through the accumulation of extracellular matrix. These models could be useful for a better understanding of pathophysiology, etiopathogenesis, and testing new methods or molecules from a preventive and therapeutic point of view.

Quantifying the fractal complexity of nutrient transport channels in Escherichia coli biofilms under varying cell shape and growth environment.

Recent mesoscopic characterization of nutrient-transporting channels in Escherichia coli has allowed the identification and measurement of individual channels in whole mature colony biofilms. However, their complexity under different physiological and environmental conditions remains unknown. Analysis of confocal micrographs of colony biofilms formed by cell shape mutants of E. coli shows that channels have high fractal complexity, regardless of cell phenotype or growth medium. In particular, colony biofilms formed by the mutant strain ΔompR, which has a wide-cell phenotype, have a higher fractal dimension when grown on rich medium than when grown on minimal medium, with channel complexity affected by glucose and agar concentrations in the medium. Osmotic stress leads to a dramatic reduction in the ΔompR cell size but has a limited effect on channel morphology. This work shows that fractal image analysis is a powerful tool to quantify the effect of phenotypic mutations and growth environment on the morphological complexity of internal E. coli biofilm structures. If applied to a wider range of mutant strains, this approach could help elucidate the genetic determinants of channel formation in E. coli colony biofilms.

Use of serum-free media for peripheral blood mononuclear cell culture and the impact on T and B cell readouts

IntroductionAs part of a wider programme of work developing next-generation risk assessment approaches (NGRA) using non-animal methods (NAMs) for safety assessment of materials, Unilever SEAC is exploring the use of a peripheral blood mononuclear cell (PBMC) system to investigate how cells from different arms of the human immune system are impacted by different treatments. To maximise human relevance, the cell cultures are supported by human serum, but this came with some challenges, including an inability to measure induced levels of immunoglobulins due to high background levels. Therefore, a study comparing use of human sera containing media with three different chemically defined serum-free media was undertaken.Materials and MethodsPBMC were isolated from healthy donors and cultured in the absence (media alone) or presence of stimulation reagents (CpG-ODN plus IL-15, Pokeweed Mitogen (PWM) or Cytostim (CS)), in RPMI plus human serum, AIM-V, CTS OpTmizer T cell expansion SFM or X-VIVO 15 media. T cell (CD4+ and CD8+) and B cell proliferation and viability were measured after 6 days, along with levels of total IgG in the cell culture supernatants.ResultsEach of the serum-free media tested supported good levels of viable and proliferating T cells and B cells over the 6 days of culture, with only a few, small differences across the media, when there was no stimulation. They also enabled detection of a stimulation-evoked increase in IgG levels. There were however some differences in the viability and proliferation responses of T and B cells, to different stimuli, across the different media.DiscussionThe serum-free media formulations tested in this study offer defined systems for. measuring B cell IgG responses, in vitro, in either a ‘T cell-independent’ (CpG + IL-15) or “T cell-dependent” (PWM or CS) manner and for assessing B cell proliferation, particularly in response to a “T cell-independent” stimulus. However, there are some characteristics and features endowed by human serum that appear to be missing. Therefore, further work is required to optimise animal-free, chemically defined culture conditions for PBMC based assays for inclusion in tiered safety assessments.

Bio-orthogonal tuning of matrix properties during 3D cell culture to induce morphological and phenotypic changes.

Described herein is a protocol for producing a synthetic extracellular matrix that can be modified in situ during three-dimensional cell culture. The hydrogel platform is established using modular building blocks employing bio-orthogonal tetrazine (Tz) ligation with slow (norbornene, Nb) and fast (trans-cyclooctene, TCO) dienophiles. A cell-laden gel construct is created via the slow, off-stoichiometric Tz/Nb reaction. After a few days of culture, matrix properties can be altered by supplementing the cell culture media with TCO-tagged molecules through the rapid reaction with the remaining Tz groups in the network at the gel-liquid interface. As the Tz/TCO reaction is faster than molecular diffusion, matrix properties can be modified in a spatiotemporal fashion simply by altering the identity of the diffusive species and the diffusion time/path. Our strategy does not interfere with native biochemical processes nor does it require external triggers or a second, independent chemistry. The biomimetic three-dimensional cultures can be analyzed by standard molecular and cellular techniques and visualized by confocal microscopy. We have previously used this method to demonstrate how in situ modulation of matrix properties induces epithelial-to-mesenchymal transition, elicits fibroblast transition from mesenchymal stem cells and regulates myofibroblast differentiation. Following the detailed procedures, individuals with a bachelor's in science and engineering fields can successfully complete the protocol in 4-5 weeks. This protocol can be applied to model tissue morphogenesis and disease progression and it can also be used to establish engineered constructs with tissue-like anisotropy and tissue-specific functions.

Essentials and Pertinence of Cold Plasma in Essential Oils, Metal–Organic Frameworks and Agriculture

ABSTRACTCold atmospheric pressure plasma (CAPP) comprises an ensemble of ionized gas, neutral particles, and/or reactive species. Electricity is frequently used to produce CAPP via a variety of techniques, including plasma jets, corona discharges, dielectric barrier discharges, and glow discharges. The type and flow rates of the carrier gas(es), temperature, pressure, and vacuum can all be altered to control the desired properties of the CAPP. Since a few decades ago, CAPP has become a widely used technology with applications in every walk of life. The plasma activated liquid mediums like water, ethanol, and methanol have been merged as novel sterilizers. With recent advancements in material science, particularly work on metal–organic frameworks (MOFs), essential oils, and agricultural technologies, CAPP has become a vital component of these advancements. Likewise, CAPP has been found as a green and benign technology to induce early seed germination and plant development. This review covers the critical components of CAPP, the production of reactive oxygen and nitrogen species, and mechanisms by which CAPP‐based technologies are applied to agricultural products, MOFs, and essential oils.

Improvement of the Sand Quality by Applying Microorganism Induced Calcium Carbonate Precipitation to Reduce Cement Usage

This research aimed to study the utilization of microorganisms in the soil. These microorganisms were applied to improve the quality of soil and sand to reduce cement consumption. The process of microbial-induced precipitation of calcium carbonate (MICP) was used in this study, a bonding process to create a binding between sand particles from the naturally occurring processes of microorganisms. The study was conducted to determine the maximum growth rate of bacteria (maximum growth curve) of five strains as follows Proteus mirabilis TISTR 100, Bacillus thuringiensis TISTR 126, Staphylococcus aureus TISTR 118, Bacillus sp. TISTR 658 and Bacillus megaterium TISTR 067 in Nutrient Broth (NB) culture medium at 37°C. Christensen's Urea Agar slant (UA) was a preliminary screen for urease-producing bacteria. The color change of indicator color was seen in the slant, comparing the results (+) and control (-). The researchers have selected bacterial strains capable of producing significant amounts of enzymes to hydrolyze urea. It was found that the amount of calcium carbonate sediment produced by five strains of bacteria, namely Proteus mirabilis TISTR 100, Bacillus thuringiensis TISTR 126, Staphylococcus aureus TISTR 118, Bacillus sp. TISTR 658 and Bacillus megaterium TISTR 067 had the amount of sediment produced as follows: 3.430, 3.080, 2.590, 1.985, and 1.615 mg/ml, respectively. It was found that the species Bacillus sp. TISTR 658 does not produce the most calcium carbonate sediment. Nevertheless, it made the sand samples stick together tightly and form the perfect lumps. Therefore, improving the sand's composition has shown the potential to apply the MICP process to reduce the cement used.

A Study on iPSC-Associated Factors in the Generation of Hepatocytes.

Hepatocytes are an attractive cell source in hepatic tissue engineering because they are the primary cells of the liver, maintaining liver homeostasis through their intrinsic function. Due to the increasing demand for liver donors, a wide range of methods are being studied to obtain functionally active hepatocytes. iPSCs are one of the alternative cell sources, which shows great promise as a tool for generating hepatocytes. This study determined whether factors associated with iPSCs contributed to variation in hepatocyte-like cells derived from iPSCs. The factors of concern for the iPSCs included the culture system, the source of iPSCs, and cell seeding density for initiating the differentiation. Our results found iPSC-dependent variances among differentiated hepatocyte-like cells. The matrix used in culturing iPSCs significantly impacts cell morphologies, characteristics, and the expression of pluripotent genes, such as OCT4 and SOX2, varied in iPSCs derived from different sources. These characteristics, in turn, play a consequential role in determining the functional activity of the iPSC-derived hepatocyte-like cells. In addition, cell seeding density was observed to be an essential factor for the efficient generation of iPSC-derived hepatocyte-like cells, with 2- 4 × 10 cells/cm of seeding density resulting in good morphology and functionality. This study provides the baseline of effective differentiation protocols for iPSC-derived hepatocyte-like cells with the appropriate conditions, including cell culture media, iPSC source, and the seeding density of iPSCs.

Comparison of Four Different DNA Isolation Methods from MGIT Culture for Long-Read Whole Genome Sequencing of Mycobacterium tuberculosis

Background: Tuberculosis (TB) remains a global health challenge, particularly due to drug resistance and limitations in rapid diagnosis. Next-generation sequencing (NGS), especially long-read whole genome sequencing (WGS), shows promise for rapidly detecting TB and drug resistance, but it requires high-quality DNA, which is difficult to extract from Mycobacterium tuberculosis due to its complex cell wall. Objectives: This study evaluated four DNA isolation methods for extracting pure DNA from M. tuberculosis, aiming to standardize protocols for long-read WGS. Methods: Mycobacterium tuberculosis H37RV colonies were grown in BACTEC MGIT liquid medium. Two pellets were prepared as the initial material for the DNA extraction protocol: Pellets from 1 mL McFarland 2 suspensions and all growing colonies from two MGIT liquid cultures. Four DNA extraction methods were used: The cetyltrimethylammonium bromide (CTAB) method, GeneJET Genomic DNA Purification Kit, Quick-DNA Fecal/Soil Microbe Kit, and Genematrix Tissue/Bacterial DNA Purification Kit, with some modifications. DNA quality was assessed based on concentration, purity, and integrity. Results: Among the tested methods, the Quick-DNA Fecal/Soil Kit yielded approximately 85 ng/mL of DNA and a purity of 1.9 at 260/280 nm from the colonial pellet of two MGIT tubes. However, lower intact DNA [DNA integrity number (DIN) ~ 6.8] was obtained with this kit. The CTAB method provided the highest intact DNA (DIN ~ 9.5), although the purity of the DNA was not sufficient. Conclusions: Based on three repetitions of McF-2 and colonial pellet extractions, the Quick-DNA Fecal/Soil Kit yielded the highest DNA quantity and purity but showed lower integrity compared to other methods, indicating the need for adjustments. A pellet from two MGIT cultures (~ 100 µL) is suitable for long-read WGS with this kit. However, a larger sample size is required to generalize these findings. For effective long-read sequencing of M. tuberculosis, DNA extraction protocols must be optimized to balance yield, fragment size, and purity for accurate sequencing and drug resistance analysis.

Ly6E on tumor cells impairs anti-tumor T-cell responses: a novel mechanism of tumor-induced immune exclusion

BackgroundLymphocyte antigen 6 complex, locus E (Ly6E) has been initially demonstrated to involve in T cell activity and impair viral infectivity. Recently, high expression levels of Ly6E have been reported in tumor microenvironment (TME) of various types of cancers. However, the immunoregulatory mechanism of Ly6E manipulating TME remains unknown.MethodsTCGA database and Kaplan–Meier plotter database were used to evaluate the correlation between Ly6E expression levels and cancer patient survival. After analyzing Ly6E expression levels in human breast cancer tissues and tumor cell lines, we generated Ly6E knockout (KO) and overexpression (OE) mouse cell lines. Cell proliferation ability in vitro and the ability of growth and metastasis in mouse tumor models were compared between KO/OE and wild-type tumor cells. On day 7 after tumor implantation, tumor tissues were separated for flow cytometric assay, bulk RNA sequencing and single-cell RNA sequencing (ScRNA-seq). The role of Ly6E-expressing tumor cell on macrophage was analyzed in vitro.ResultsOur result surprisingly found that high Ly6E expression levels were associated with CD8+ T cell exclusion in tumor tissues and resistance to immunotherapy. Our data showed that knockout of Ly6E in tumor cells prompts tumor regression and inhibits tumor metastases, and Ly6E-OE tumor cells vice versa. The enhanced anti-tumor effect of Ly6E knockout in tumor cells was dependent on T cell response and formed long-lasting memory. The increase in the CD8+ T-cell infiltration into the tumor islet of Ly6E-KO tumors confirmed the role of Ly6E on T cell exclusion. ScRNA-seq analysis showed that M2 macrophages are particularly abundant in the Ly6E-expressing tumor tissues, especially M2-4 macrophage cluster identified by high levels of Arg-1, indicates that Ly6E-expressing tumor cells might restrict T cell infiltration via M2 macrophages. Moreover, in vitro assay showed that cell culture media derived from Ly6E-positive tumor cells promoted macrophage migration and M2 polarization.ConclusionOur study illuminated that Ly6E-expressing tumor cells facilitated the accumulation of M2 macrophages in TME, which contributes to CD8+ T cell exclusion and provides new insights for improving efficacy of cancer immunotherapy.