Total Isolation Research Articles

Investigating the Suitability of Mare's Milk-Derived Exosomes as Potential Drug Carriers.

Exosomes are cell-derived, membrane-surrounded particles that deliver bioactive molecules to various cells. Due to their small size, low immunogenicity, extended blood circulation, and involvement in cellular communication, they hold potential as effective drug carriers. Exosomes are present in various biological fluids, including mare's milk, a traditional drink in Central Asia. This study aims to compare exosome isolation methodologies and determine the stability of mare's milk-derived exosomes as potential therapeutic carriers. Three extraction methods-immunoprecipitation, size exclusion chromatography, and total exosome isolation-were compared in terms of exosome characteristics, purity, and content. The isolated exosomes were then loaded with quercetin, and their ability to increase its bioavailability was tested in vitro and in vivo. Total exosome isolation was identified as the most efficient method for producing high-quality exosomes. These exosomes were loaded with quercetin and compared to free quercetin and exosomes alone. Exosomes loaded with 80 µM quercetin significantly restored β-galactosidase activity and cellular viability in doxorubicin-treated cells, exhibiting similar potency to 160 µM free quercetin. In aged model animals, treatment with quercetin-loaded exosomes resulted in significantly less acute and subacute damage to the myocardium, kidneys, and liver compared to untreated control animals. This study provides a proof-of-concept that mare's milk-derived exosomes can be effectively absorbed by cells and animal tissues, supporting their potential use as drug carriers.

The Distribution of Respiratory Viral Pathogens Among the Symptomatic Respiratory Tract Infection Patients From Dhaka City in the Pre-COVID-19 Pandemic Era.

Rapid and accurate diagnosis is crucial for determining the etiology and, perhaps, effectively treating and preventing viral respiratory infections. A multiplex quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay⁠⁠⁠⁠⁠⁠⁠ was utilized to determine the prevalence of viral etiology in cases of acute respiratory tract infections (ARTIs). Outpatient department (OPD) and intensive care unit (ICU) patients with fever and respiratory symptoms were enrolled from December 2018 to April 2020. Nucleic acids were extracted from the respiratory tract samples using the SV Total RNA Isolation System (Promega Corporation, Madison, WI), and virus identification was performed using qRT-PCR assay (Fast Track Diagnostics {FTD} Respiratory Pathogens, Esch-sur-Alzette, Luxembourg). A total of 152 samples were collected from OPD and ICU. Among them, 32.23% (n = 49) of the patients were positive for at least one respiratory virus. From 49 infected cases, 42 had only a single viral pathogen, whereas seven had co-infections. Of the patients, 32.25% (30) in the OPD and 32.20% (19) in the ICU tested positive for the respiratory viral pathogen. Among the OPD patients, human coronaviruses (HCoVs) OC43, 229E, NL63, and HKU1were detected as predominant viruses (10.75%), followed by influenza virus (IFV) (8.6%), human rhinoviruses (HRVs) (6.45%), human parainfluenza viruses (HPIVs) (6.45%), respiratory syncytial virus (RSV) (3.22%), and adenovirus (2.15%). In ICU cases, HPIV and HRV were detected as predominant viruses (8.47% each), followed by HCoV (5.08%), human metapneumovirus (HMPV) (5.08%), influenza A virus (IAV) (3.38%), adenovirus (3.38%), and RSV (1.69%). This study highlighted the prevalence of respiratory viruses in both the community and hospital settings during pre-COVID-19, indicating a significant presence among patients in these environments.

Multilingual Complexities in the Origins and Development of the Harrist Movement and Its Worship Patterns in Ivory Coast

The Harrist Church in Ivory Coast, West Africa, emerged from the ministry of Liberian William Wadé Harris who baptized between 10,000 and 200,000 people during his eighteen-month evangelistic tour, 1913–1915. This story is full of linguistic complexities and anomalies. Harris himself spoke only English and his own local Liberian Glebo language. He was therefore compelled to work through expatriate English-speaking merchants, knowledgeable of and conversant in local languages, as interpreters and translators in addressing the twelve ethnic groups who heard and accepted his message. Harris encouraged new converts to compose hymns in their own indigenous languages by transforming musical genres embedded in their local musical traditions. Additionally fascinating is that during this early colonial period, the twelve ethnic groups impacted by Harris’s ministry lived in almost total isolation from each other and developed their own hymn traditions for thirty-five years (1914–1949), unaware of the existence of churches and worship patterns in neighboring ethnic districts. Only in 1949 did they suddenly become acquainted with the broader, multi-musical, multilingual reality of the Harrist movement. Since then, individual musicians and choirs from local congregations have gradually begun to sing a few of each other’s songs, though the challenge of becoming a truly multicultural, multiethnic church remains a work in progress. Documentation of these developments include written colonial and early Protestant and Catholic missionary sources and a large number of eye-witness interviews. Primary research methods employed here come from four intersecting disciplines and theoretical frameworks: orality studies, with particular focus on oral sources in constructing historical narrative; religious phenomenology; mission history; and ethnodoxological research.

PSIII-2 Exploring differential gene expression and pathways associated with pregnancy outcomes in beef heifers

Abstract Heifer fertility is a key factor in the success of beef production systems, as the reproductive performance of a heifer correlates with her stayability in the breeding herd. However, despite being reproductively mature and physically healthy, 5 to 15% of these heifers fail to conceive within a designated breeding season. The underlying physiological mechanisms preventing these heifers from achieving pregnancy remain elusive. Therefore, this study aimed to determine differentially expressed genes (DEGs) and biological pathways associated with pregnancy outcomes in beef heifers. Angus-Simmental crossbred heifers were subjected to an estrus synchronization and fixed-time artificial insemination (AI) program (7-d CO-Synch + CIDR) and blood samples were collected at the time of AI for isolation of peripheral white blood cells (PWBC). After pregnancy check, heifers were classified as pregnant (P) and non-pregnant (NP). Based on that, 6 animals per group were randomly selected for total RNA isolation from the PWBC samples, and genome-wide expression was measured through RNA sequencing. The RNA-Seq data were analyzed using an in-house bioinformatics pipeline, with filtered reads aligned to the Bos taurus reference genome using STAR. DEGs were identified using DESeq2, followed by functional analysis using ShinyGO. Our approach unveiled 230 DEGs, comprising 102 up and 128 downregulated genes in the NP group (P-value ≤ 0.05 and |log2FC| > 0.5). Upregulated genes included those from the cytochrome P450 superfamily (CYP27B1 and CYP2U1). The genes SCML2, USIG2, and FBP1 were upregulated and have been associated with immune response and increased PWBC counts. This may be related to the over-representation of biological processes involved in cell division based on the upregulated genes. KEGG pathway over-representation analysis of DEGs retrieved allograft rejection, graft-versus-host disease, type I Diabetes Mellitus, insulin signaling pathway, and transcriptional misregulation of cancer. These pathways included genes such as BOLA-DQB, PRKAR1B, CALML4 and JUP, which were reported as downregulated during times of inflammatory response. Another downregulated gene was GZMB, which is needed for proper cell targeting during immune response. This finding may provide a link between immune function and early pregnancy failure. However, the relationship between the immune system and pregnancy warrants further investigation. Our results shed light on the molecular mechanisms underlying reproductive performance in beef heifers and support previous studies associating immune function with pregnancy outcomes. These differentially expressed genes may be further explored as potential avenues for enhancing fertility in beef production systems.

PSI-6 Early life programming of the bovine jejunum function in response to maternal vitamin and mineral supplementation

Abstract Despite the increased appreciation of the involvement of maternal nutrition in fetal development, its effects on jejunum programming remain largely unexplored. Here, we investigated the impact of maternal vitamin and mineral supplementation throughout gestation on the differential gene expression and underlying biological pathways in the jejunum of neonatal calves. For this, beginning 60 d before breeding and continuing throughout gestation, crossbred Angus heifers (n = 14) were fed either a basal diet (CON; n = 7) or the basal diet plus 113 g•heifer-1•d-1 of VTM supplement (VTM; n = 7). All heifers were gestating female calves, which were euthanized 30 h after birth. Samples of jejunum mucosa were collected, stored at -80°C, then subjected to total RNA isolation and RNA sequencing. After quality control, the reads were mapped using STAR aligner and differentially expressed genes (DEGs) were identified using DESeq2. Maternal VTM supplementation did not affect calf organ mass, including jejunum weight. However, high-resolution respirometry analysis revealed greater mitochondrial efficiency in jejunum of calves from VTM supplemented dams. Additionally, we identified 528 DEGs between the VTM and CON calves (P-value ≤ 0.05 and |log2FC| > 0.5). Among them, the genes IGFBP2 and IGFBP6, which are key genes in insulin pathway and involved in regulation of insulin-like growth factors (IGF), IGF transport, and uptake, were upregulated in the VTM group. Additional pathways were identified using ShinyGO, which included the pancreatic secretion pathway, over-represented by genes such as PLCB1, CCK, and SLC26A3. The gene PLCB1 has been associated with feed efficiency, growth, and carcass traits in multiple species. Likewise, the SLC26A3 gene encodes a key intestinal chloride anion exchanger associated with enhanced feed efficiency in cattle. Genes encoding signaling molecules involved with immune response, T cell activation, and defense response were also among the DEGs upregulated in the VTM calves, including the TNFSF18 and TNFRSF4 genes. Our findings suggest that maternal prenatal vitamin and mineral supplementation throughout gestation affects the expression of genes involved in the jejunum function of offspring at a neonatal time point. The long-term consequences of these changes, however, warrant further investigation.

Comparative analysis of high-throughput RNA extraction kits in Naïve Non-Human Primate (NHP) tissues for downstream applications utilizing Xeno Internal Positive Control (IPC)

Ribonucleic acid (RNA) extraction and purification play pivotal roles in molecular biology and cell and gene therapy, where the quality and integrity of RNA are critical for downstream applications. Automated high-throughput systems have gained interest due to their potential for scalability and reduced labor requirements compared to manual methods. However, ensuring high-throughput capabilities, reproducibility, and reliability while maintaining RNA yield and purity remains challenging.This study evaluated and compared the performance of four commercially available high-throughput magnetic bead-based RNA extraction kits across six types of naïve non-human primate (NHP) tissue matrices: brain, heart, kidney, liver, lung, and spleen. The assessment focused on RNA purity, yield, and extraction efficiency (EE) using Xeno Internal Positive Control (IPC) spiking.Samples (∼50 mg) were homogenized via bead-beating and processed according to the manufacturer's protocol on the KingFisher Flex platform in eight replicates. RNA purity and yield were measured using a NanoDrop® spectrophotometer, while EE was evaluated via real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR).The findings indicate consistent high RNA purity across all tested extraction kits, yet substantial variation in RNA yield. Extraction efficiency exhibited variations across tissue types, with decreasing trends observed from brain to lung tissues. These results underscore the importance of careful kit selection and method optimization for achieving reliable downstream applications. The MagMAX™ mirVana™ Total RNA Isolation Kit stands out as the most accurate and reproducible, making it the preferred choice for applications requiring high RNA quality and consistency. Other kits, such as the Maxwell® HT simplyRNA Kit, offer a good balance between cost and performance, though with some trade-offs in precision. These findings highlight the importance of selecting the appropriate RNA isolation method based on the specific needs of the research, underscoring the critical role of accurate nucleic acid extraction in gene and cell therapy research.In conclusion, this study highlights the critical factors influencing RNA extraction performance, emphasizing the need for researchers and practitioners to consider both kit performance and tissue characteristics when designing experimental protocols. These insights contribute to the ongoing efforts to enhance the reproducibility and reliability of RNA extraction methods in molecular biology and cell/gene therapy applications.

From primers to pipettes: An immersive course introducing high school students to qPCR for quantifying chemical defense gene expression.

We created a 2-week, dual-module summer course introducing high school students to environmental toxicology by teaching them quantitative polymerase chain reaction (qPCR) as a way to quantify gene expression of chemical defense proteins in response to exposure to environmental pollutants. During the course, students are guided through the various stages of a successful qPCR experiment: in silico primer design and quality control, total RNA extraction and isolation, cDNA conversion, primer test PCR, and evaluation of results via agarose gel electrophoresis or UV/Vis spectra. The course combines lectures, discussions, and demonstrations with dry and wet laboratory sections to give students a thorough understanding of the scope, utility, and chemical principles of qPCR. At the end of the course, the students are taught how to analyze qPCR data and are encouraged to discuss their findings with other classmates to evaluate their hypotheses and assess possible sources of error. This course was designed to be easily adaptable to multiple test species, chemical exposures, and genes of interest. To explore both terrestrial and aquatic toxicology, the students use honey bees (Apis mellifera) and mosquitofish (Gambusia affinis) as test organisms, as well as ABC-type efflux transporters, antioxidant enzymes, and cytochrome P450 enzymes as endpoints for assessing gene expression. We share this course setup and applied protocols to encourage others to design and offer similar courses that give high school students a hands-on introduction to a broad swath of environmental toxicology research and an opportunity to develop scientific skills necessary for university-level research.

Phytoplasma Associated with White-backed Planthopper on Rice Plants in Sidrap Regency, South Sulawesi

South Sulawesi is one of the largest rice production centers in Indonesia. Several important diseases of rice plants, such as those caused by viruses and phytoplasmas, can be transmitted by insect vectors, especially leafhoppers and stem plant. Symptoms of diseases caused by viruses and phytoplasmas are quite diverse but visually similar and difficult to distinguish. This study aims to analyze the presence of phytoplasma associated with white-backed planthopper which are commonly found in rice plantations. The research method used is by conducting surveys and explorations of insect samples in six villages in Sidrap District. White-back planthoppers found on rice plantations showing symptoms of yellowing and stunted leaves were sampled for further analysis, including total DNA isolation of insects, standard PCR amplification for insect and Nested-PCR for phytoplasma identification, gene sequencing for both amplicons, and nucleotide analysis using BLAST method and Mega X program. The PCR with CO1 primer successfully amplified a 700 bp amplicon from insects, whereas nested-PCR using fP1/rP7 primers followed by m23SR/R16F2n amplified phytoplasma supposedly around 1800 bp and 1250 bp of 16S RNA gene, respectively. The DNA sequencing analysis results indicate that the insect samples were identified as 83% Sogatella vibix species based on homology percentage analysis using BLAST and Mega X Program. As for the phytoplasma, it leans more towards the 16SrI group or Candidatus phytoplasma asteris (Aster yellows phytoplasma) with a homology percentage of 99%.

INVESTIGATION OF THE RELATIONSHIP OF DL-PHENYLALANINE AND DL-ALANINE WİTH THE HEDGEHOG PATHWAY IN THE PROSTATE CANCER CELL LINE (PC-3)

OBJECTIVE: In this study, it was aimed to investigate the effect of DL-Phenylalanine and DL-Alanine on the Hedgehog signaling pathway on the PC-3 prostate cancer cell line. MATERIAL AND METHODS: The effects of DL-Phenylalanine and DL-Alanine on cell viability in PC-3 cancer cells were determined by the MTT method. The IC50 value determined for DL-Phenylalanine was applied to PC-3 and HEK-293 cells. Total RNA isolation and cDNA synthesis were performed. Gene expression of key genes related to the Hedgehog pathway (SHH, PTCH, SMO, GLI-1) was determined by qPCR (Quantitative PCR). RESULTS: DL-Alanine showed no cytotoxic effect on PC-3 cells. DL-Phenylalanine decreased cell viability in a time- and dose-dependent manner. The IC50 value for DL-Phenylalanine was determined to be 500 μg/mL at 48 hours. After DL-Phenylalanine application in PC-3 cells, down-regulation in the expression of all genes was detected, while up-regulation was detected in HEK-293 cells (p<0.05). CONCLUSIONS: DL-Phenylalanine inhibited the Hedgehog pathway in prostate cancer cells. This inhibition was not observed in the control group HEK-293 cells. While DL-Phenylalanine may be a therapeutic candidate for the treatment of prostate cancer, DL-Alanine was not found to have such an effect.

Freezing Diluted Bovine Serum Albumin Standards Does Not Significantly Affect Standard Curves.

Total protein isolation followed by quantitation is a common protocol in many laboratories. Quantitation is often done using a colorimetric assay such as the bicinchoninic acid (BCA) assay in which a change in the color of the BCA reagent is related to protein concentration. Extracted protein samples are compared to a standard curve made with dilutions of a protein standard such as bovine serum albumin (BSA) to determine their concentrations. A series of experiments was designed to determine the most reproducible and accurate method for quantifying protein concentrations of samples in an experimental series over time. The effect of freezing on diluted standards was investigated. Standards were frozen at -20°C or -80°C and serially thawed and refrozen up to three times prior to their use in a BCA assay. Thawing and refreezing the standards had no significant effect on protein concentration and the resulting standard curves. Inter-person and intra-person variability in the preparation of standards was also investigated. Protein concentration differences due to inter-person and intra-person variability were greater than protein concentration variability resulting from freezing and thawing, regardless of the freezing temperature. The most reproducible and accurate method for determining the protein concentration of extracted samples in an experimental series over time is diluting a large batch of BSA standards and freezing them at either -20°C or -80°C. Reproducibility was maintained with up to three freeze-thaws.

Development of Mycological Medium using Tomato Juice Extract as Principal Base

Study’s Novelty/Excerpt This study introduces an approach to mycological media development by utilizing Tomato Juice Extract (TJA) as a primary base, highlighting its rich nutrient profile and potential for sustainable, cost-effective fungal cultivation. The research uniquely demonstrates the influence of various TJA concentrations on fungal growth, revealing selective preferences for certain fungi and emphasizing the importance of medium optimization. These findings provide significant insights into the potential of natural sources in microbiological practices, laying the groundwork for future studies to further optimize TJA and explore its practical applications in mycology. Full Abstract This project focused on developing mycological media using the primary base of Tomato Juice Extract (TJA). Tomatoes contain a rich mix of vitamins, minerals, and organic acids, creating an ideal environment for cultivating various fungi. Various concentrations of Tomato Juice Agar (TJA) and Potato Dextrose Agar (PDA) were prepared (200 mL, 300 mL, and 400 mL). TJA was created by combining tomato filtrate with different sugar concentrations (10g, 15g, 20g), keeping agar agar powder constant at 20 g. Samples of soil from refuse dumpsite and spoiled bread were inoculated onto the prepared TJA and PDA (control). The total fungal counts, isolation, and identification were determined using PDA and TJA. Microscopic analyses, serial dilutions, and colony characterization provided a detailed assessment. TJA exhibited total fungal counts of 2-3 propagules/g for refuse dumpsite soil and 3-4 propagules/ml for spoiled bread. PDA yielded counts of 3-6 propagules/g for refuse dumpsite soil and 3-5 propagules/ml for spoiled bread. Various fungi, including Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger, Rhizopus stolonifer, Penicillium. digitanum, and Fusarium oxyporum were identified. TJA showed selective preferences for Aspergillus niger and Rhizopus stolonifer. This study successfully developed mycological media with tomato juice extract, yielding promising fungal cultivation results. Different TJA concentrations influenced fungal growth, thus emphasizing the importance of selecting the appropriate medium. The absence of growth of some of the test fungal isolates on TJA and exclusive isolation of Fusarium oxysporum on PDA shows medium-specific preferences. Tomato juice extract aligns with sustainability and cost-effectiveness, offering an alternative to traditional components. Valuable insights into concentration-dependent fungal growth guide future experimentation and optimization. Tomato juice extract as a mycological medium base introduces a sustainable alternative with unique nutritional profiles. Concentration-dependent fungal preferences revealed the significance of medium optimization. These findings encourage the use of natural sources for more sustainable microbiological practices. While laying innovative mycological media groundwork, further research is needed to optimize tomato juice agar fully. Mycological media development with tomato juice extract offers practical benefits in cost-effectiveness and sustainability.

Identification of DNA Barcodes from rbcL Chloroplast DNA in Katokkon Chili (Capsicum annuum var. chinense) Origin of Tana Toraja, South Sulawesi

Katokkon chili (Capsicum annuum var. chinense) is a type of chili which are commonly found in Tana Toraja. It has a distinctive aroma, high spiciness, and a potential economic value but has not been widely identified and explored, thus, it is necessary to carry out molecular identification using DNA barcodes from chloroplast DNA. The aim of this study was to determine genetic variation and the results of constructing a phylogenetic tree from DNA sequences katokkon chili (C. annuum var. chinense) using the rbcL marker. This study used 6 samples of katokkon chilies (C. annuum var. chinense) and 3 outgroup samples (C. frutescens, C. chinense and C. baccatum). The stages of the research included total DNA isolation, qualitative and quantitative tests, PCR amplification using rbcL primers, and sequencing. Data analysis used is sequence alignment, phylogenetic, genetic distance matrix, haplotypes and phylogeography. The results showed genetic variation with 7 polymorphisms consisting of 4 singleton sites at the nucleotide base sequences of 6th, 525, 715 and 737, and 3 parsimony informative sites at the nucleotide base sequences 370, 616 and 902 and the haplotype distribution is divided into 4 haplotypes namely Hap_1 (A1, A2, A3, B1, B2 and B3), Hap_2 (C1), Hap_3 (C2), and Hap_3 (C3). The phylogenetic tree construction formed two clades, namely clade I consist of six samples of katokkon chilies (C. annuum var. chinense) and clade II consisting of three outgroup samples. Mark the highest bootstrap is 96 and the lowest bootstrap value is 29. Genetic distance matrix values are in the range of 0.000–0.005.

Genetic Diversity of Panulirus Versicolor in the Waters of Barrang Caddi Island, Makassar Strait, South Sulawesi, Indonesia

Barong shrimp or lobster (Panulirus versicolor) is a fishery commodity with high economic value and great demand. This study aims to determine the genetic characteristics of Panulirus versicolor at the fishing location in the waters of Barrang Caddi Island, Makassar Strait, using primers LCO-1490F and HCO-2198R. Genomic DNA extraction was performed using a Quick-DNA Tissue Miniprep Kit for total isolation. For DNA purity, the elution buffer utilized in this research was specifically selected for its suitability for PCR amplification with KOD FX Neo, providing optimal conditions for efficient genetic analysis. The primary genes used were LCO-1490F with primers GGT CAA CAA ATC ATA AAG ATA TTG G, and HCO-2198R with TAA ACT TCA GGG TGA CCA AAA AAT CA. The study utilized a 1% agarose gel in a 1X TBE buffer at 50 voltage for 45 minutes to move the total DNA and PCR products. The analysis results at sampling stations 0.2-03 showed increasingly smaller genetic distances. Based on the results of BLASTn analysis, each station had the same type of Panulirus versicolor with a similarity of 99-100%. The morphological characteristics included a carapace with a black spot and black and white lines on each abdominal segment. The analysis of genetic variation in the lobster population on Barrang Caddi Island using primers LCO-1490F and HCO-2198R obtained a DNA fragment of 700 bp. The population of Panulirus versicolor lobster on Barrang Caddi Island showed a high level of similarity or low diversity.

Transplantation techniques for liver resections in children

Aim. To carry out a retrospective analysis of the treatment outcomes of the patients who underwent liver resection with angioplasty facilitated by transplantation techniques. Materials and methods. The sample of cases was divided into four groups: liver resection with total vascular isolation of the liver, ante situm liver resection, hepatic artery and portal vein reconstruction, cardiopulmonary bypass resection. The analysis was focused on surgery features and treatment outcomes. Results. The study involved 29 patients. The performed interventions included 11 liver resections with total vascular isolation, 6 ante situm liver resections, 7 resections with angioplasty, and 5 cardiopulmonary bypass resections. 5 patients (17 %) developed complications that required reoperation. Within 90 days, 4 patients (14 %) died. For patients with malignant neoplasms, one-, three-, and five-year overall survival rates accounted for 84.4 %, 58.4 %, and 51.1 %; one-year event-free survival rate comprised 57.1 %, and three- and five-year event-free survival was 41.7 %.The study revealed no significant differences in the complication rates. The groups of ante situm liver resections and cardiopulmonary bypass resections significantly differed from the other groups by the higher incidence of tumor progression, invasion of adjacent organs, hemorrhagic complications, preoperative stay, and duration of cold perfusion of the liver. The cardiopulmonary bypass resections were noted to have higher duration of surgery, vascular isolation, heparin use, and the frequency of anticoagulant therapy before surgery. Conclusion. Liver resections with total vascular isolation, angioplasty and transplantation techniques are considered as the only possible treatment option for a number of patients. Further accumulation of results will reduce the risk of adverse outcomes.

Evaluation and Standardization of RNA Extractions with Quality for RNA-Seq for Balamuthia mandrillaris

Balamuthia mandrillaris is a free-living amoeba (FLA) that causes granulomatous amebic encephalitis (GAE) and skin lesions. Transcriptomic analysis is a powerful tool used to study B. mandrillaris pathogenic infections. However, preliminary tests of RNA extraction showed poor results, so it has become essential to standardize a protocol for high-quality RNA. The present study evaluated 11 RNA extraction protocols based on three commercial kits by making modifications to the temperature and centrifugation times, and by combining kits. Four protocols, namely Q3 (based on QIAGEN RNeasy Mini Kit, with modifications in temperature and centrifugation times), T1 (Invitrogen TRIzol Reagent), T2 (combination of TRIzol and QIAGEN modified protocols) and T3 (combination of TRIzol and PROMEGA SV Total RNA Isolation protocols), presented RNA with good integrity and purity, except for the T1 protocol, which obtained an A260/230 value below the acceptable threshold. High RNA integrity (RIN) values were obtained with the Q3 (9.8), T2 (9.2), and T3 (8.9) protocols, while the T1 protocol obtained a lower RIN value (7.1). The Q3, T2, and T3 protocols obtained high-quality RNA from B. mandrillaris based on the criteria of integrity, purity, and concentration, where the implemented modifications and combinations raised the quality; thus, their use is recommended to obtain accurate results when performing transcriptomic analysis.

Identification of Circular RNAs as Biomarker Candidates in Lung Cancer Treatment.

Lung cancer is the most common malignancy and among the leading cause of cancer death worldwide. Therefore, there is an important need for biomarkers that can be used in the early diagnosis of the disease and in the follow-up of treatment. Circular RNAs (circRNAs) have a covalently closed circular structure that lacks 3' and 5' polar ends and is resistant to RNAase enzymes. Due to these properties, they can be stably found in body fluids. Therefore, they can serve as potential biomarkers in the diagnosis, monitoring of therapeutic response and prognosis of cancer. In our study, we aimed to investigate the expression levels of circRNA molecules in the treatment of lung cancer and to determine those that have the potential to be biomarkers. In this in vitro study, expression levels of 163 circRNAs were investigated in A549 cells, a non-small cell lung cancer cell line, before and after treatment with carboplatin and pemetrexed. Total RNA isolation and cDNA synthesis were performed after treatments. Expression levels of circRNA genes were determined by RT-qPCR method with the designed divergent primer sequences. The study revealed the characterisation of differentially expressed circRNAs by treatment in lung cancer cells. Of them, hsa_circ_0001320 is not expressed in cancer cells, is expressed only after treatment, and increased the level of its expression in response to combination therapy. As a result, while carboplatin, pemetrexed, and combined drug applications changed the expression levels of some circRNAs in lung cancer cells, some circRNAs were expressed only after treatment. In treatment follow-up and management, hsa_circ_0001320 has been identified as potential biomarker candidate.

Characterization of the prevalence of Salmonella in different retail chicken supply modes using genome-wide and machine-learning analyses

Salmonella is a foodborne pathogen that causes salmonellosis, of which retail chicken meat is a major source. However, the prevalence of Salmonella in different retail chicken supply modes and the threat posed to consumers remains unclear. The prevalence, serotype distribution, antibiotic resistance, and genomic characteristics of Salmonella in three supply modes of retail chicken (live poultry, frozen, and chilled) were investigated using whole-genome sequencing (WGS) and machine learning (ML). In this study, 480 retail chicken samples from live poultry, frozen, and chilled supply modes in Guangzhou from 2020 to 2021, as well as 253 Salmonella isolates (total isolation rate = 53.1 %), were collected. The prevalence of isolates in the live poultry mode (67.5 %, 81/120) was statistically higher than in the frozen (50.0 %, 120/240) and chilled (43.3 %, 52/120) (P < 0.05) modes. Serotype identification showed significant differences in the serotype distribution of Salmonella in different supply modes. S. Enteritis (46.7 %) and S. Indiana (14.2 %) were predominant in the frozen mode. S. Agona (23.5 %) and S. Saintpaul (13.6 %) were predominant in live poultry, while S. Enteritis (40.4 %) and S. Kentucky (17.3 %) were predominant in chilled mode. Antibiotic testing showed that frozen mode isolates were more resistant; the multidrug-resistant (MDR) rate of isolates in the frozen mode reached 91.8 %, significantly higher than in the chilled (86.5 %) and live (74.1 %) (P < 0.05) modes. WGS was performed on 155 top serotypes (S. Enteritidis, S. Kentucky, S. Indiana, and S. Agona). The antibiotic resistance gene analysis showed that the abundance and carrying rate of antibiotic resistance genes of Salmonella in the frozen mode (54 types, 16.1 %) were significantly higher than in other modes (live poultry: 36 types, 9.4 %, P < 0.05; chilled: 31 types, 11.6 %). The blaNDM-1 and blaNDM-9 genes encoding carbapenem resistance were found in frozen mode isolates on a complex transposon consisting of TnAS3-IS26. Virulence factors and plasmid replicons were abundant in the studied frozen mode isolates. In addition, single nucleotide polymorphism (SNP) phylogenetic tree results showed that in the frozen supply mode, the S. Enteritidis clonal clade continued to contaminate retail chicken meat and was homologous to S. Enteritidis strains found in farm chicken embryos, slaughterhouse chicken carcasses, and patients from hospitals in China (SNP 0 = 10). Notably, the pan-genome-based ML model showed that characteristic genes in frozen and live poultry isolates differed. The narZ gene was a key characteristic gene in frozen isolates, encoding nitrate reductase, relating to anaerobic bacterial growth. The ydgJ gene is a key characteristic gene in the live mode and encodes an oxidoreductase related to oxidative function in bacteria. The high prevalence of live poultry mode Salmonella and the transmission of frozen mode MDR Salmonella in this study pose serious risks to food safety and public health, emphasizing the importance of improving disinfection and cold storage measures to reduce Salmonella contamination and transmission. In conclusion, the continued surveillance of Salmonella across different supply models and the development of an epidemiological surveillance system based on WGS is necessary.

Contact lenses as novel tear fluid sampling vehicles for total RNA isolation, precipitation, and amplification.

The tear fluid is a readily accessible, potential source for biomarkers of disease and could be used to monitor the ocular response to contact lens (CL) wear or ophthalmic pathologies treated by therapeutic CLs. However, the tear fluid remains largely unexplored as a biomarker source for RNA-based molecular analyses. Using a rabbit model, this study sought to determine whether RNA could be collected from commercial CLs and whether the duration of CL wear would impact RNA recovery. The results were referenced to standardized strips of filtered paper (e.g., Shirmer Strips) placed in the inferior fornix. By performing total RNA isolation, precipitation, and amplification with commercial kits and RT-PCR methods, CLs were found to have no significant differences in RNA concentration and purity compared to Schirmer Strips. The study also identified genes that could be used to normalize RNA levels between tear samples. Of the potential control genes or housekeeping genes, GAPDH was the most stable. This study, which to our knowledge has never been done before, provides a methodology for the detection of RNA and gene expression changes from tear fluid that could be used to monitor or study eye diseases.

Abstract B019: Identification of gene signatures predictive of response to Ad-IFNα/Syn3 in bladder cancer

Abstract Introduction: Interferon α gene therapy (Ad-IFNα/Syn3) is FDA approved for treatment of BCG-unresponsive non-muscle invasive bladder cancer. Ad-IFNα/Syn3 is a non-replicating adenovirus that when transduced into target tissues, produces IFNa2b protein with anti-tumor activity. In the phase 3 multicenter trial, 45.5% of patients with carcinoma-in-situ and 60% of those with Ta/T1 disease who had a complete response to Ad-IFNα/Syn3 at 3 months remained recurrence free at 12 months. Targeting mechanisms of resistance and identifying predictive biomarkers to improve patient selection and overall response rates is a top priority. Towards this, we treated 29 human bladder cancer cell lines with Ad-IFNα/Syn3 and assessed their responses to therapy. We identified sensitive and resistant cell lines and gene signatures predictive of response. Methods: Human bladder cancer cell lines were grown in MEM supplemented with 10% FBS in 96-well plate. After overnight attachment, these were treated with Ad-IFNα/Syn3 (MOI 1000) and cell titre glow assay was performed 72h post-treatment. Cells were also seeded in 6-well plates. and after 24h cell-free supernatants were collected for ELISA and cells were collected for RNA isolation using RNAqueous Total RNA Isolation kit (Thermo Fisher). RNA quality was assessed using Tapestation. RNAseq analysis was carried out using Ion proton Sequencer. Ingenuity pathway analysis (IPA) and gene set enrichment were performed on the sequencing data for the cell lines. ELISA was used to measure IFNα and IL6 protein levels in cell free supernatants. We also tested organoids developed from bladder cancer patients to test drug efficacy and identify gene signatures. Results: Out of the 29 cell lines, we identified that sensitivity to Ad-IFNα/Syn3 was pronounced in luminal cells (8/13 luminal cell lines). Most basal cells were either resistant (&amp;gt;70% viability) or only moderately sensitive to Ad-IFNα/Syn3 (between 70-40% viability) when compared to control. We selected 7 cell lines for sequencing and ELISA measurements: luminal cell lines BV, UC6, Rt4V6 and UC5, and basal cell lines ScaBER, HT1197, and T24. All cell lines mentioned above could be successfully transduced by the adenoviral vector as measured by increased expression of IFNα protein in the cell-free supernatants. Ad-IFNα/Syn3-sensitive luminal cell lines at baseline had lower IFNα and IFNγ scores when compared to resistant basal cell lines. We identified several cell-death pathways enriched in treated cells that were sensitive to Ad-IFNα/Syn3. IL6 measurements in cell free supernatants revealed increased expression of IL6 after treatment in sensitive cells. However, in resistant cells IL6 expression was either high at baseline (ScaBER) or both undetectable at baseline and after treatment (UC5). Conclusion: Our results suggest that the luminal cell lines are more sensitive to Ad-IFNα/Syn3 and that high baseline expression of IFNα and IFNγ in basal cell lines contributes to resistance. IL6 levels are also predictive of response to Ad-IFNα/Syn3. Citation Format: Morgan E. Pierce, Alexis R. Steinmetz, Aruna Nannapaneni, Tanner S. Miest, David J. McConkey, Sharada Mokkapati, Colin P.N. Dinney. Identification of gene signatures predictive of response to Ad-IFNα/Syn3 in bladder cancer [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr B019.

Storage implications on the microbiological quality of some locally manufactured pharmaceuticals

Pharmaceutical products non-sterile are expected to have a minimal microbial load which must not exceed the limits as stated in pharmacopoeia monographs. This study attempted to evaluate storage implications on the microbiological quality of some non-sterile pharmaceutical products manufactured locally in some states in south east Nigeria. Twenty brands of pharmaceutical products comprising 13 tablets, 5 capsules and 2 suspension procured from patent medicine and local drug markets in Aba and Enugu states were stored at room temperature (25oC) for 6 months. Microbial growth was evaluated at 0 and 6 months using standard microbiological procedures including Total aerobic bacteria plate count, isolation, characterization and identification of microbial contaminants. The results from the study showed that 55% and 30% of the pharmaceutical products had bacteria and fungi contamination at 0 month which increased to 70% and 50% at 6 months storage period respectively. Statistical analysis showed there was a significant increase (p &lt; 0.05) in growth of micro-organisms at 6 months for both bacteria and the fungi/moulds (p &lt; 0.05). The isolated bacteria were Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus mirabilis, Escherichia coli while the fungi include Trichosporonasahii, Curvularia bothriochloae, Candida albicans, Candida parapsilosis. All contaminated samples had microbial counts above the British Pharmacopoeia (BP) acceptabl limit of 103 and 102 CFU/ml for bacteria and fungi respectively. This can be attributed to poor adherence to current Good Manufacturing Practice (cGMP) by the manufacturers. Thus, it is recommended that manufacturers adhere strictly to cGMP and storage conditions stated on these pharmaceutical products followed strictly during distribution and storage to reduce the levels of microbial contamination.