Blood Kit Research Articles

Culture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urine.

Urinary Tract Infections (UTIs) are among the most prevalent infections globally. Every year, approximately 150million people are diagnosed with UTIs worldwide. The current state-of-the-art diagnostic methods are culture-based and have a turnaround time of 2-4 days for pathogen identification and susceptibility testing. This study first establishes an optical density culture-based method for spiking healthy urine samples with the six most prevalent uropathogens. Urine samples were spiked at clinically significant concentrations of 103-105 CFU/ml. Three DNA extraction kits (BioStic, PowerFood, and Blood and Tissue) were investigated based on the DNA yield, average processing time, elution volume, and the average cost incurred per extraction. After DNA extraction, the samples were sequenced using MinION and Flongle flow cells. The Blood and Tissue kit outperformed the other kits based on the investigated parameters. Using nanopore sequencing, all the pathogens and corresponding genes were only identified at a spike concentration of 105 CFU/ml, achieved after 10min and 3 hours of sequencing, respectively. However, some pathogens and antibiotic-resistance genes (ARG) could be identified from spikes at 103 colony formation units (CFU/mL). The overall turnaround time was five hours, from sample preparation to sequencing-based identification of pathogen ID and antimicrobial resistance genes. This study demonstrates excellent promise in reducing the time required for informed antibiotic administration from 48 to 72h to five hours, thereby reducing the number of empirical doses and increasing the chance of saving lives.

CLONAL HEMATOPOIESIS AND ITS ROLE IN THE DEVELOPMENT OF CARDIOVASCULAR DISEASES

Clonal hematopoiesis (CH) is the increase in somatic clones carrying mutations in hematopoietic stem cells. This biological condition can lead to cancer and is implicated in the development of atherosclerosis and cardiovascular diseases. CH of indeterminate potential (CHIP) refers to somatic mutations in genes that are associated with the development of Coronary heart disease (CHD) and leukemia. Now, with next-generation sequencing, we can detect mutations even if they are present in only a small number of cells in the tissue sample being studied. Consequently, numerous studies have shown that mutations in the DNMT3A, TET2, ASXL1, and JAK2 genes found in the blood are associated with coronary heart disease. The purpose of our study is to detect a genetic variant of genes in Kazakh patients with atherosclerosis, which will further allow us to study the role of CHIP in increasing the risk of developing coronary microvascular dysfunction and CHD. We perform high-throughput whole-exome sequencing in patients with atherosclerosis. The object of the study is samples delivered from the clinic “National Scientific Cardiac Surgery Center” in Astana. The study is carried out in accordance with the principles of the Declaration of Helsinki of the World Medical Association. Genomic DNA extraction was performed on 245 samples using the Illustra Blood Kit (Cytiva, USA). Qualitative and quantitative assessment of the extracted genomic DNA was conducted using the NanoDrop 2000 (Thermo Scientific) and Qubit 2.0 (Thermo Fisher Scientific). Subsequently, DNA library preparation was carried out using the Illumina DNA Prep with Exome 2.5 Enrichment kit. Quality control of the resulting DNA libraries was conducted on a 2100 Bioanalyzer system using the Agilent DNA 1000 Kit and High Sensitivity DNA kit (Agilent Technologies). Following assessment of the DNA library concentration on Qubit 2.0, they were loaded onto the high-performance sequencer NovaSeq 6000 (Illumina, USA) following the manufacturer’s protocol. We conducted human whole-exome sequencing on 245 samples to identify somatic clones in the peripheral blood of patients with atherosclerosis. Patients were divided into three groups – low risk, middle, and high risk of atherosclerotic complications. Bioinformatic analysis of sequence data were performed. We created list of genes associated with CH to deep analysis and to interpreter the data in patient groups. Subsequently, DNA extraction from the remaining samples is performed, followed by sequencing on the NovaSeq 6000 platform. Analysis of the resulting sequenced data is currently underway. Further research and monitoring of CHIP will enable us to understand the mechanisms underlying the development of cardiovascular diseases and to devise a comprehensive management plan for patients with this pathology. Supported by Committee of Science of the Ministry of Science and Higher Education of Republic of Kazakhstan (AP14869903), (BR21881970) and Nazarbayev University CRP (211123CRP1608).

Preanalytical Impact of Incomplete K2EDTA Blood Tube Filling in Molecular Biology Testing.

The aim of this study was to investigate the possible preanalytical effect of incomplete filling of blood tubes on molecular biology assays. The study population consisted of 13 healthy volunteers from whom 11 mL of whole blood was collected and then distributed in different volumes (1.5, 3.0, and 6.0 mL, respectively) into three 6.0 mL spray-dried and evacuated K2EDTA blood tubes. Automated RNA extraction was performed using the Maxwell® CSC RNA Blood Kit. DNA was extracted with a MagCorePlusII, with concomitant measurement of glyceralde-hyde-3-phosphate dehydrogenase (GAPDH) gene expression. The nucleic acid concentration was calculated using the NanoDrop 1000 spectrophotometer, and purity was assessed using A260/280 and A260/230 absorbance ratios. The RNA concentration was higher in the tubes filled with 1.5 and 3.0 mL of blood than in the reference 6 mL filled tube. The RNA 260/280 and RNA 260/230 ratios did not differ significantly between the differently filled blood tubes. The DNA concentration remained constant in the differently filled tubes. Compared to the 6.0 mL reference filled tube, the 1.5 mL and 3.0 mL filled blood tubes displayed a lower DNA 260/280 nm ratio. The DNA 260/230 ratio did not differ significantly in any of the variously filled tubes. Compared to the 6.0 mL reference filled blood tube, the 1.5 mL and 3.0 mL filled blood tubes showed a significant increase in the GAPDHcycle threshold. Our results suggest that underfilling of K2EDTA blood tubes may be a modest but analytically significant source of bias in molecular biology testing.

Using Environmental DNA to Detect and Identify Sweetpotato Whitefly Bemisia argentifolii and Twospotted Spider Mite Tetranychus urticae in Greenhouse‐Grown Tomato Plants

ABSTRACTEnvironmental DNA (eDNA) consists of genetic material shed by living organisms, including those that are deceased, offering a unique opportunity to detect and identify terrestrial insect pests without requiring visual identification. The sweetpotato whitefly, Bemisia argentifolii, and the twospotted spider mite, Tetranychus urticae, are notorious for causing crop losses through virus transmission and direct feeding. Our study aimed to: (1) assess the effectiveness of B. argentifolii literature‐based PCR primers compared to newly developed primers for eDNA amplification, (2) evaluate the sensitivity of conventional PCR (cPCR) and real‐time quantitative PCR (qPCR) for detecting eDNA of B. argentifolii and T. urticae, (3) establish a rapid eDNA processing methodology using the LGC Biosearch Technologies QuickExtract DNA extraction kit and the Qiagen DNeasy Blood and Tissue kit, and (4) test the specificity of the developed primers against non‐target species. B. argentifolii and T. urticae were confined to tomato leaves (Solanum lycopersicum) using clip cages for 24 h, after which eDNA was collected from leaf surfaces using a water spray method, filtered, and processed for DNA amplification. While literature‐based primers showed sufficient sensitivity, their specificity for eDNA applications was inadequate, prompting the design of novel PCR primers for both pest species. Positive eDNA detection was achieved with both amplification methods, with qPCR proving more reliable than cPCR due to the latter's inconsistent performance with positive control samples. We also introduced a rapid eDNA processing approach using the QuickExtract DNA extraction kit, contrasting it with the more conventional Qiagen DNeasy Blood and Tissue kit. We believe that our findings are the first step toward the practical use of eDNA as a highly sensitive, early detection technique.

Optimising recovery of DNA from minimally invasive sampling methods: Efficacy of buccal swabs, preservation strategy andDNA extraction approaches for amphibian studies.

Studies in evolution, ecology and conservation are increasingly based on genetic and genomic data. With increased focus on molecular approaches, ethical concerns about destructive or more invasive techniques need to be considered, with a push for minimally invasive sampling to be optimised. Buccal swabs have been increasingly used to collect DNA in a number of taxa, including amphibians. However, DNA yield and purity from swabs are often low, limiting its use. In this study, we compare different types of swabs, preservation method and storage, and DNA extraction techniques in three case studies to assess the optimal approach for recovering DNA in anurans. Out of the five different types of swabs that we tested, Isohelix MS-02 and Rapidry swabs generated higher DNA yields than other swabs. When comparing storage buffers, ethanol is a better preservative than a non-alcoholic alternative. Dried samples resulted in similar or better final DNA yields compared to ethanol-fixed samples if kept cool. DNA extraction via a Qiagen™ DNeasy Blood and Tissue Kit and McHale's salting-out extraction method resulted in similar DNA yields but the Qiagen™ kit extracts contained less contamination. We also found that samples have better DNA recovery if they are frozen as soon as possible after collection. We provide recommendations for sample collection and extraction under different conditions, including budgetary considerations, size of individual animal sampled, access to cold storage facilities and DNA extraction methodology. Maximising efficacy of all of these factors for better DNA recovery will allow buccal swabs to be used for genetic and genomic studies in a range of vertebrates.

Development of molecular sex identification method for Asian palm civet (Paradoxurus hermaphroditus) and Small Indian civet (Viverricula indica): a step towards forensic identification

Civet coffee and perfume are premium products in demand worldwide. Consequently, the civet population is threatened by several factors (e.g., the rapidly growing trend of civets being removed from the wild and held in captivity), raising concerns about civet welfare and conservation. In light of this, our aim was to develop a molecular sex identification method for the Asian palm civet (Paradoxurus Hermaphroditus) and the Small Indian civet (Viverricula Indica). We collected five Asian palm civet tissue samples (two male, one female, and two of unknown sex) and one female Small Indian civet from the repository, Advanced Institute for Wildlife Conservation (AIWC). DNA was extracted from all tissue samples using the DNeasy Blood and Tissue Kit. For sex identification, we optimized the PCR conditions to amplify partial fragments of sex-determining region Y (Sry) and the zinc finger X (Zfx) genes using DNA from two male Asian palm civet samples. The PCR amplicons were examined on a 2% agarose gel, and two male civets showed one distinct band at 250 bp (for Sry) and another at 120 bp (for Zfx). To confirm this finding, the PCR amplicons (Sry and Zfx genes) from one male sample were sequenced and % similarity and nucleotide pairwise analysis were calculated. The Sry and Zfx sequences showed 96.99% (for Sry) and 97.78% (Zfx) similarity to the masked palm civet, the only species in the families Paradoxurinae or Viverridae for which sequence data was publicly available. These results confirmed that the optimized PCR conditions are suitable for amplifying the Sry and Zfx genes in the Asian palm civet, which will be helpful for sex identification. Subsequently, we used this optimized method for the sex identification of three Asian palm civets and one Small Indian civet sample obtained from the repository, AIWC. Additionally, we used the method for identification of sex in a seized civet tissue sample received for forensic analysis. This report is the first to focus on developing a method for identifying the sex of Asian palm civets and Small Indian civets. This method will be helpful for researchers working on the ecology and conservation of civet population.

Molecular Characterization of the Presence of Bovine Papillomavirus in Cattle Teat Warts and a Different Treatment Approach

Background: Papillomatosis is a skin condition that is distinguished by benign proliferative tumors with a complicated etiology and epithelial proliferation. There is a need to perform a more thorough study on bovine papillomavirus and identify the virological properties of the agent in detail since a definitive treatment approach against this infection has not yet been completely identified and the suggested treatment outcomes differ. Methods: Samples were collected from warts developing on the teats of 500 cattle raised for milk production in Burdur Center and its districts. The samples were defrosted in order to extract DNA and the Dneasy Blood and Tissue Kit was used for the extraction procedure. By using a PCR assay, wart sample extracts were examined for 13 different BPV types (excluding BPV Type 7). For BPV type-specific primers, a protocol was utilized. Amplification products were demonstrated using agarose gel electrophoresis. Result: In the PCR test of 500 wart samples, BPV types (type 1-type 13) were detected in 378 (75.6%). In the general distribution of BPV types (single or mixed types) in teat warts, BPV-2 (n=85; 22.49%), BPV-8 (n=45; 11.90%), BPV-9 (n=48; 12.70%) and BPV-10 (n=52; 13.76%) were determined to be more common. In the study; it was determined that three different combined treatments provided 100% regression or complete recovery in warts developing on the teat of cattle. In conclusion; one of these three treatment combinations may be preferred for teat wart lesions in cattle.

First Report of Erwinia aphidicola Causing Bulb Rot of Onion in Chile.

During the 2021-22 and 2022-23 seasons (December to February), onion plants (Allium cepa L.) showing decay, leaf blight, chlorosis and water soak lesions were collected in Central Chile. Five symptomatic plants were sampled from 20 different onion fields. Brown rot of the external scales was observed in bulbs from two fields: one planted with the cv. Campero (20 ha; O'Higgins Region), and another with cv. Marenge (2 ha; Metropolitan Region). The disease incidence in these fields ranged from 2% to 5%. Isolations were carried out from symptomatic leaves and bulbs from these fields on King's B medium, resulting in small white colonies with smooth margin. Three isolates were selected, two from first field (QCJ3A & QCJ2B), and one from second field (EPB1). A preliminary identification based on 16S rRNA sequences was conducted. BLAST analyses of strains QCJ3A, QCJ2B and EPB1 (GenBank Accession No. PP345601 to PP345603) against the NCBI Database resulted in a match with strains (GenBank Accession No. ON255770.1 and ON255825.1) isolated from infected bulbs in Texas, USA identified as Erwinia spp. (Khanal et al. 2023), with 100% coverage and 100% identity (707 bp out of 707). To evaluate the pathogenicity of these three strains, onion bulbs were inoculated (Guajardo et al. 2023). Toothpicks previously immersed in a bacterial suspension at ~ 108 colony forming units (CFU)/mL were pricked at a 4 cm depth into the shoulders of onion bulbs bought from commercial store and incubated at room temperature. Bulbs inoculated with sterile water served as negative control. A known onion bulb rotting bacterial strain of Dickeya sp. was used as a positive control. At the end of the incubation period (20 days), bulbs were opened longitudinally across their inoculation site, showing that the external scales had a brown color. Negative control remained asymptomatic. Strains were re-isolated from damaged tissue and identified as Erwinia sp. This assay was repeated three times with the same results. For further identification, genomic DNA extraction was carried out using the Blood & Cell Culture DNA Kit (Qiagen), and genome sequencing was performed in the Illumina HiSeq 2500 platform. The Whole Genome Shotgun project for strains QCJ3A, QCJ2B and EPB1 have been deposited at DDBJ/ENA/GenBank under the accession JBANEI010000000, JBANEJ010000000 and JBANEK010000000. The average nucleotide identity (ANI) values were 99.6% (EPB1), 98.2% (QCJ2B), and 99.6% (QCJ3A) and DNA-DNA hybridization (dDDH) values were 96.9% (EPB1), 83.7% (QCJ2B), and 97.1% (QCJ3A), when compared with the type strain Erwinia aphidicola JCM 21238 (GenBank accession No. GCF_014773485.1). The three strains were deposited in the Chilean Collection of Microbial Genetic Resources (CChRGM). Erwinia aphidicola has been previously described causing diseases in common bean (Phaseolus vulgaris) and pea (Pisum sativum), in Spain (Santos et al. 2009) and in pepper (Capsicum annuum) in China (Luo et al. 2018). Its close relative E. persicina has been reported causing bulb rot in onion in Korea (Cho et al. 2019) and garlic in Europe (Galvez et al. 2015). To our knowledge, this is the first report of E. aphidicola causing a bulb rot of onion in Chile. Although the distribution and prevalence of this bacterium in Chilean agroecosystems is not known, it can be a potential cause of losses in onions and other crops such as beans, peas, and peppers. Additional studies should be conducted to determine the host range of Chilean Erwinia aphidicola strains.

Detection of single-nucleotide polymorphisms in growth hormone and insulin-like growth factor-1 genes related to growth traits in purebred and crossbred quails.

There is a limited amount of research conducted on quail breeding domestically and internationally, particularly at the molecular level. This study aimed to detect single-nucleotide polymorphisms in the growth hormone (GH) and insulin-like growth factor-1 (IGF-1) genes across two quail varieties and their hybrids correlate these genetic factors with body weight (BW) and growth rate at 0 and 6 weeks, and assess crossing effects. White and Japanese quail were crossed. Simultaneously producing pure varieties and crosses (genotypes) was achieved through this breeding strategy. Fifty females from each genotype were randomly selected for blood sampling. Genomic DNA was extracted and amplified from the blood using the DNeasy blood kit (Qiagen, Germany). Nucleotide polymorphism between quail genotypes was determined through DNA sequencing. Two types of alleles (A and B) for the GH gene in quails showed significant genotypic differences (AA, BB, and AB). The quail carried a mutated IGF-1 gene. For growth traits, substantial positive heterosis was detected. The genotype AA had the highest BW and weight gain. The white variety can act as a sire, and both white and Japanese varieties can function as dams to improve growth traits. The growth characteristics of the hybrids surpassed those of the original varieties.

Pupal Exuviae of Culex Pipiens L. (Diptera: Culicidae) Can be Utilised as a Non-Invasive Method of Biotype Differentiation

BackgroundCulex pipiens L. is a principal vector of zoonotic arboviruses in Europe, acting in both an amplification role in enzootic transmission between avian hosts and as a bridge vector between avian hosts and mammals. The species consists of two forms which are indistinguishable using morphological methods but possess varying ecological and physiological traits that influence their vector capacity. In this study we validate methods that can be used to extract trace DNA from single pupal exuviae of Cx. pipiens for use in molecular speciation of samples. These DNA extraction methods are compared using measurement of the total yield and successful identification using a real-time polymerase chain reaction (PCR) assay.ResultsGenomic DNA was initially extracted from colony-derived individuals using an ethanol precipitation method, two commercially available DNA extraction kits: DNeasy® Blood & Tissue Kit (Qiagen, UK) and Wizard® SV Genomic DNA Purification System (Promega, UK) and a direct real-time PCR method. Time elapsed between eclosion and processing of pupae significantly influenced Cx. pipiens form identification as nucleic acid concentration and PCR amplification success decreased with increased time elapsed. Real-time PCR amplification success, however, was not shown to vary significantly between the three extraction methods, with all methods successfully identifying all samples, but the direct real-time PCR method achieved a lesser amplification success rate of 70% (n = 20 for each treatment). More variable results were produced when field-derived exuviae were used, with no significant difference in real-time PCR amplification success found across the four methods and a lower overall rate of successful identification of 55–80%.ConclusionsThis study shows that both colony and field derived Cx. pipiens pupal exuviae can be a useful non-invasive source of trace DNA permitting accurate biotype differentiation for at least twenty-four hours post-eclosion. The significance and utility of this technique in ecological and behavioural studies of Cx. pipiens is discussed and recommendations made for use according to experimental scenario.

Detection of rat lungworm (Angiostrongylus cantonensis) infection by real-time PCR from the peripheral blood of animals: a preliminary study

Rat lungworm disease or neuroangiostrongyliasis is a cerebral parasitic infection that affects humans and animals alike. Its clinical signs and symptoms can range from mild self-resolving to serious life-threatening conditions. Studies suggest therapeutic interventions during the early stages of infection to be more effective than in later stages. However, early diagnosis of infection is usually problematic without the knowledge of exposure and/or detection of the parasite’s DNA or antibody against the parasite in the cerebrospinal fluid. This requires a lumbar puncture, which is an invasive procedure that generally requires hospitalization. This study evaluates an affordable and less invasive alternative to detect parasitic DNA by PCR from the peripheral blood of potentially infected animals. Blood samples from 58 animals (55 dogs and 3 cats) with clinical suspicion of infection were submitted to our lab between February 2019 and August 2022 by local, licensed veterinarians. DNA was extracted from whole blood, plasma, serum, and/or packed cells using the Qiagen DNeasy Blood & Tissue Kit as per the manufacturer’s protocol. All 58 animals were tested by real-time PCR using the AcanITS1 assay and 32 of these animals (31dogs; 1 cat) were also tested using the AcanR3990 assay. The PCR results for both assays were classified into strongly positive > positive > weakly positive > negative, and equivocal for ambiguous results, based on the strength of the signal. The percent infection detected using the AcanITS1 and AcanR3990 assays was 12.72% (7/55) and 20.68% (6/29), respectively. The overall percent infection detected was 34.37% (11/32), with only two animals testing positive by both assays. The three cats involved in this study tested negative by both assays. These results are promising and warrant further investigations to increase sensitivity including variables that might affect detection in the blood, such as parasite load, and laboratory methodologies.

Assessment of nucleic acid extraction protocols for antibiotic resistance genes (ARGs) quantification in aircraft wastewater

This study evaluated ten nucleic acid extraction protocols (EP1 to EP10) for measuring five endogenous antibiotic resistance genes (ARGs) in four aircraft wastewater samples (AWW1 to AWW4). The targeted ARGs, including blaCTX-M, blaNDM-1, ermB, qnrS, and tetA, encompassed highly and minimally abundant ARGs. TetA and ermB were consistently detected across four aircraft wastewater samples using the DNeasy Blood and Tissue Kit and the AllPrep PowerViral DNA/RNA kit. QnrS displayed high detection rates with specific extraction protocols and aliquot volumes. Concentrations of ARGs varied across aircraft wastewater samples, with differing extraction protocols influencing quantitative results. The concentrations of tetA, ermB, and qnrS in AWW1 were distinct, while AWW2 to AWW4 exhibited a broader range for tetA, ermB, qnrS, blaCTX-M, and blaNDM-1. EP1 consistently produced the highest concentrations for several ARGs. Collective data analysis revealed varying ARG concentrations across the ten extraction protocols, suggesting the importance of careful extraction protocol selection in ARG monitoring in aircraft wastewater samples. Based on the results, we suggest that a small sample volume (as low as 0.2 mL) may be sufficient for ARG characterization in aircraft wastewater samples. The findings also emphasize the need for considering toilet paper removal without compromising nucleic acid extraction efficiency. The study highlights promising prospects for aircraft wastewater monitoring of ARGs, calling for further investigation into the import and spread of unique ARGs through transport hubs.

Regulation of the Novel MSTN-GAL3-NOX1 Axis Reverses Obesity-Induced Skeletal Muscle Quality Decline Resulting in Improved Glycemic Indices and Restored Angiogenesis Following Ischemia

Objective: To test the hypothesis that restored muscle quality achieved through myostatin KO improves angiogenesis in obese mice through the resolution of GAL3-NOX1-mediated endothelial dysfunction.Methods: db/db mice, a well-described model of obesity, were crossed with mice lacking myostatin (MSTN KO), a myokine that negatively regulates muscle differentiation and growth, galectin-3 (GAL3 KO), a pro-inflammatory/atherogenic RAGE (receptor for advanced glycation endproducts), and NADPH oxidase-1 (NOX1 KO), a TGF-b-stimulated primary producer of the reactive oxygen species (ROS) O2−, to generate db+/−-MSTN+/−, db+/−-GAL3+/−, and db+/−-NOX1+/− mice. We utilized nuclear magnetic resonance (NMR) spectroscopy to assess skeletal muscle (SKM) lean/fat content in db+/−-MSTN+/− mice. Muscle and plasma lipid content were analyzed via mass spectrometry. Mice were placed in metabolic cages and monitored with CLAMS (Comprehensive Lab Animal Monitoring System) in order to determine their whole-body metabolism. Insulin metabolism indices were determined via appropriate blood and plasma testing kits. Morphology of SKM was determined via microscopy of H&E and Mason’s Trichrome-stained gastrocnemius cross sections. Femoral artery ligation was used to stimulate in vivo angiogenesis in response to hind limb ischemia (HLI); whereas 1mm aortic rings cultured in ECBM (2% FBS) were used to study ex vivo angiogenesis. Gene expression was assessed by RNA-Seq and RT-qPCR. Results: MSTN deletion results in significantly increased SKM mass and restored SKM quality (i.e. morphology and metabolic function) without altering whole-body mass, fat percentage, or activity in obese (db−) mice. We observed that obesity inhibits and MSTN KO restores angiogenesis in both HLI and aortic ring assay models. Previous studies in our lab revealed that MSTN deletion was suffcient to restore endothelial function in db/db mice. Additionally, our lab has shown that GAL3 or NOX1 KO in db/db mice phenocopied the vascular improvements seen in db−-MSTN− mice without restoring SKM size or quality. RNA-Seq and RT-qPCR analysis of SKM and endothelial cells (ECs) revealed significant upregulation of GAL3 and NOX1 expression in db−-MSTN+ mice but not in db−-MSTN− and db−-GAL3− mice. Finally, either GAL3 or NOX1 deletion results in amended angiogenesis in obese animals. Conclusion: In summary, restoration of muscle quality in obese individuals provides potent protection of vascular and metabolic health. A correlate of this improvement is the attenuation of a novel MSTN-GAL3-NOX1 axis, which we have shown to mediate vascular inflammation/redox signaling in obesity. These data suggest that pharmacological targeting of upstream MSTN, downstream GAL3 and/or NOX1 could be effective in treating cardiovascular disease in the context of obesity and metabolic syndrome. A. C. Speese is supported by NIH 1F31HL165858-01A1. D.W. Stepp and D. J. Fulton are supported by NIH 1R01HL147159. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

First Report of Cucurbit Yellow Vine Disease Caused by Serratia marcescens on Cucurbit Crops in Iowa

Cucurbit yellow vine disease (CYVD) is caused by Serratia marcescens, vectored by squash bugs (Anasa tristis), and is an emerging disease in many parts of the U.S. CYVD can cause 100% yield losses in cucurbits (Bruton et al., 2003). In the summer of 2021, at the Iowa State University Horticultural Research Station (HRS) in Gilbert, Iowa, we observed leaf yellowing, vine decline, and honey-brown discoloration of the phloem of acorn squash (Cucurbita pepo cv. Table Ace) plants in research fields that were infested with squash bugs. In 2022, we observed similar symptoms on pumpkin (Cucurbita maxima cv. Howden) and muskmelon (Cucumis melo cv. Athena) in different fields at the HRS and on giant pumpkins (Cucurbita maxima cv. Prizewinner) in Jones and Ringgold counties. For up to 3 symptomatic plants of each cucurbit species per location, a 20-cm-long stem section immediately above the soil line was excised, surface sterilized by immersion in 10% sodium hypochlorite and 70% ethanol for 2 min each, then triple rinsed in sterile water. The interior of the cross-section tissue was blotted on Luria agar amended with cycloheximide (100 μg/ml) and tetracycline (20 μg/ml) (Stock et al. 2003). Whitish translucent colonies developed after incubation at 28°C for 48 h. The genomic DNA of three isolates from symptomatic plants of muskmelon (MK01), pumpkin (HFP01), and giant pumpkin (AP01), was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Germantown, MD). S. marcescens species-specific primers YV1 (5’-GGGACTTGCTCCCCGG-3’) and YV4 (5’-AACGTCAATTGATGAACGTATTAAGT-3’) (Bruton et al. 2003) were used to amplify part of the 16S rDNA gene, and the primers specific to S. marcescens CYVD strains A79F/A79R (Zhang et al., 2005) were used to amplify part of a major facilitatory superfamily (MFS) transporter gene strain. The sequences of the 16S rRNA PCR product for the three isolates were identical and were deposited in NCBI under Accession OR963533. They shared 100% (395/395 nt) identity with other CYVD strains (Rascoe et al. 2003) and those of other S. marcescens strains in NCBI. The sequences of the amplified region of the MFS transporter gene of the three isolates (NCBI Accession OR962261) were identical and showed a 98.8% (319/323 nt) identity to that of non-CYVD-causing S. marcescens strains, such as N10A28 (Accession CP033623.1). Koch’s postulates were fulfilled by inoculating C. pepo cv. Zephyr plants with either strain HFP01 or phosphate buffer saline (PBS) (10 plants per treatment) 1 wk after seeding by injecting 300 µl of bacteria (~108 CFU/ml) or PBS using a syringe needle. Plants were incubated at 28°C in a growth room for 4 wks. CYVD symptoms similar to those observed in the field developed on 7 out of 10 plants inoculated with strain HFP01 in one study, and 9 out 10 plants in a replicate study, with none of the PBS-inoculated plants showing CYVD symptoms. Bacteria were isolated from the symptomatic plants with selection on tetracycline. The PCR fragments amplified with YV1/YV4 and A79F/A79R were the same size as those of the pre-inoculation strain HFP01. To our knowledge this is the first report of CYVD in Iowa and in the Upper Midwest of the U.S. CYVD is a devastating disease that poses a significant threat to cucurbit production. This report can serve as an alert for the region’s growers and for the development of effective management practices.

Guardians of Neurons: The Cntf Gene and Ciliary Neurotrophic Factor (CNTF) in the Genetic Landscape of Alzheimer’s Disease Neuroprotection

Background: Type II Diabetes Mellitus (Type II DM) is a complex systemic disorder that affects various organs and has been strongly associated with an increased risk of cognitive impairments, including dementia. The Ciliary Neurotrophic Factor (CNTF) gene is implicated in the pathophysiology of diabetes-induced cognitive decline, suggesting its potential as a biomarker for neurodegenerative diseases. Objective: The primary objective of this study was to investigate the expression of the CNTF gene in diabetic patients with dementia and to evaluate its correlation with cognitive dysfunction. Methods: A cohort of 88 diabetic dementia patients and 12 healthy controls was selected based on inclusion criteria. CNTF serum levels were measured using Chemiluminescent immunoassay (CLIA), and CNTF gene expression was assessed through real-time PCR. DNA was isolated using the QIAgen blood kit, followed by bisulfite DNA modification and Methylation Specific PCR for methylation profiling. Data analysis included comparative studies using GraphPad Prism 9.0 with statistical significance set at a p-value of <0.05. Results: The study found that CNTF serum levels in diabetic dementia patients (n=88) were significantly lower at 4.98 µg/mL compared to 14.21 µg/mL in healthy controls (n=12). MMSE scores were also reduced in the patient cohort, averaging 10.98 versus 25.6 in controls. A notable decrease in CNTF gene expression was observed with a fold change of approximately 4.1 in diabetic dementia patients, indicating underexpression in this group. Conclusion: CNTF gene expression is inversely correlated with cognitive function in diabetic patients, suggesting that CNTF could serve as a useful biomarker for the early detection of dementia in this population. The identification of this gene's role opens new avenues for targeted therapeutic interventions and enhances the understanding of dementia's etiology in diabetic patients.

Vitamin D Deficiency and Its Association With Vitamin D Receptor Gene Variants Among Malaysian Women With Hypertensive Disorders in Pregnancy: Protocol for a Nutrigenomics Study.

Vitamin D deficiency has been associated with hypertensive disorders in pregnancy (HDP). The risk of developing HDP was reported to be further augmented among individuals with a vitamin D receptor (VDR) genetic variant. However, the reported roles of VDR variants in hypertensive disorders are inconsistent among different populations. Given the relatively higher incidence of vitamin D deficiency among Malaysian pregnant women and the high incidence of HDP in this population, we hypothesize that there may be associations between the risk of vitamin D deficiency and HDP with VDR genetic variants. This paper outlines the protocol for a study to determine the association of vitamin D status and VDR sequence variants among Malaysian pregnant women with HDP. This prospective study consists of two phases. The first phase is a cross-sectional study that will entail gathering medical records, a questionnaire survey, and laboratory testing for vitamin D status, with a planned recruitment of 414 pregnant women. The questionnaire will be utilized to assess the risk factors for vitamin D deficiency. The vitamin D status will be obtained from measurement of the vitamin D (25-hydroxyvitamin D3) level in the blood. The second phase is a case-control study involving a Malay ethnic cohort with vitamin D deficiency. Participants will be divided into two groups with and without HDP (n=150 per group). Genomic DNA will be extracted from the peripheral blood monocytes of participants using the Qiagen DNA blood kit, and VDR sequence variants will be determined using polymerase chain reaction-high-resolution melting (PCR-HRM) analysis. Sanger sequencing will then be used to sequence randomly selected samples corresponding to each identified variant to validate our PCR-HRM results. The VDR genotype and mutation frequencies of BsmI, ApaI, TaqI, and FokI will be statistically analyzed to evaluate their relationships with developing HDP. As of December 2023, 340 subjects have been recruited for the phase 1 study, 63% of whom were determined to have vitamin D deficiency. In the phase 2 study, 50 and 22 subjects have been recruited from the control and case groups, respectively. Recruitment is expected to be completed by March 2024 and all analyses should be completed by August 2024. The outcome of the study will identify the nonmodifiable genetic components contributing to developing vitamin D deficiency leading to HDP. This will in turn enable gaining a better understanding of the contribution of genetic variability to the development of HDP, thus providing more evidence for a need of customized vitamin D supplementation during pregnancy according to the individual variability in the response to vitamin D intake. ClinicalTrials.gov NCT05659173; https://clinicaltrials.gov/study/NCT05659173. DERR1-10.2196/53722.

Principles and Limitations of miRNA Purification and Analysis in Whole Blood Collected during Ablation Procedure from Patients with Atrial Fibrillation.

Background: MicroRNA (miRNA) have the potential to be non-invasive and attractive biomarkers for a vast number of diseases and clinical conditions; however, a reliable analysis of miRNA expression in blood samples meets a number of methodological challenges. In this report, we presented and discussed, specifically, the principles and limitations of miRNA purification and analysis in blood plasma samples collected from the left atrium during an ablation procedure on patients with atrial fibrillation (AF). Materials and Methods: Consecutive patients hospitalized in the First Department of Cardiology for pulmonary vein ablation were included in this study (11 with diagnosed paroxysmal AF, 14 with persistent AF, and 5 without AF hospitalized for left-sided WPW ablation-control group). Whole blood samples were collected from the left atrium after transseptal puncture during the ablation procedure of AF patients. Analysis of the set of miRNA molecules was performed in blood plasma samples using the MIHS-113ZF-12 kit and miScript microRNA PCR Array Human Cardiovascular Disease. Results: The miRNS concentrations were in the following ranges: paroxysmal AF: 7-23.1 ng/µL; persistent AF: 4.9-66.8 ng/µL; controls: 6.3-10.6 ng/µL. The low A260/280 ratio indicated the protein contamination and the low A260/A230 absorbance ratio suggested the contamination by hydrocarbons. Spectrophotometric measurements also indicated low concentration of nucleic acids (<10 ng/µL). Further steps of analysis revealed that the concentration of cDNA after the Real-Time PCR (using the PAXgene RNA Blood kit) reaction was higher (148.8 ng/µL vs. 68.4 ng/µL) and the obtained absorbance ratios (A260/A280 = 2.24 and A260/A230 = 2.23) indicated adequate RNA purity. Conclusions: Although developments in miRNA sequencing and isolation technology have improved, detection of plasma-based miRNA, low RNA content, and sequencing bias introduced during library preparation remain challenging in patients with AF. The measurement of the quantity and quality of the RNA obtained is crucial for the interpretation of an efficient RNA isolation.

DNA barcoding of Burgo chicken from Bengkulu, Indonesia, based on the cytochrome oxidase gene sub unit I mitochondria DNA

Abstract. Utama AF, Jarulis, Sipriyadi, Jannah IM. 2023. DNA barcoding of Burgo chicken from Bengkulu, Indonesia, based on the cytochrome oxidase gene sub unit I mitochondria DNA. Biodiversitas 24: 6268-6275. The Burgo chicken provides a genetic source of one crossbreed chicken in Bengkulu Province. However, genetic information on Burgo chickens is not yet available, while the population of this chicken continues to decline. Research on DNA barcoding using the cytochrome oxidase subunit I mtDNA gene was conducted to obtain DNA barcodes and the relationship between Burgo chickens and other chicken species based on the COI mtDNA gene. Blood samples were obtained from Burgo chickens belonging to the Bengkulu Burgo chicken hobbyist community. Collected blood was isolated following the dneasy® blood and tissue kit protocol based on the spin-column protocol procedure, Qiagen. Amplification of genomic DNA using Polymerase Chain Reaction. The product was electrophoresed on a 1.2% agarose gel and visualized under UV light using Gel Documentation System, Axygen. Samples with bright DNA bands proceeded to the sequencing process. Sequencing results were analyzed using MEGA 11.0 software. The results showed that the target length of the Burgo chicken band was in accordance with the primer design used (752pb). SNPs were obtained at 10 specific sites in Burgo chickens and had a species barcode at site 746. The intraspecies genetic distance was 0.6%, interspecies 1.2%, and with the outgroup 14.5%, there were 12 haplotypes from all samples (n=15). Based on the result, we can conclude that the Burgo chicken is closely related to the red jungle fowl compared to other chicken species.

Characterizing Hereditary Hemolytic Anemias in a Hispanic Cohort Using Next Generation Sequencing

Background: Hereditary hemolytic anemias (HHA) are a heterogeneous group of nonimmune disorders characterized by increased red blood cell (RBC) destruction due to abnormalities of hemoglobin stability, defects of RBC metabolism, and disorders of RBC hydration. Although uncommon, they comprise important causes of anemia in children and adults by causing chronic or episodic hemolysis. Clinical, laboratory, and genetic heterogeneity characterize this group of disorders and make recognition challenging. The advent of next generation sequencing (NGS) has made accurate genetic diagnoses attainable, with an increasing number of studies reporting clinical utility in HHA. For patients with suspected HHA, multigene testing is available incorporating an NGS panel associated genes. However, there is limited data on the use of multigene NGS to characterize HHA in the Hispanic population. Herein, we describe results from NGS testing of a pilot cohort referred for HHA investigation to hematology clinics along the US/Mexico border. Methods: Pediatric and adult hematology clinics at Texas Tech University in El Paso, TX collaborated for testing on HHA referral and clinical case review. The diagnostic panel (AnemiaID/PerkinElmer/Revvity®) included 51 genes encoding RBC cytoskeletal proteins, membrane transporter, RBC enzymes, and certain bilirubin metabolism genes. The complete coding region, splice site junctions, and, where appropriate, deep intronic or regulatory regions were covered. Targeted gene capture and library construction for NGS were performed using a Whole Blood and Saliva kit and 150 base pair paired-end sequencing was done on Illumina® NGS systems at target average coverage of 80×. NGS output data were summarized descriptively for all patients and clinically correlated for diagnosis. Results: In this pilot cohort, 11 patients were tested during September 2022 to June 2023, age ranging 7-75 years, with females accounting for 64% of the group. Findings are reported in the Table below; Pathogenic variants leading to a definitive diagnosis were identified in 8 of 11 cases (73%). The most frequently mutated genes were SPTA1 followed by PIEZO1, SPTB, RHAG, GSR, SLC4A1 and TPI1. Approximately 58% of the mutations were reported as novel. Diagnoses included, most commonly, Hereditary Spherocytosis followed by Hereditary Pyropoikilocytosis and Congenital Dyserythropoietic Anemia. Compound heterozygosity leading to complex interactions was noted in 4 cases (36%), involving SPTA1 low expression alleles in trans (alpha-LELY and alpha-LEPRA) in 2 cases. Conclusion: Hereditary hemolytic anemia in the Hispanic population is characterized by complex molecular interactions and a high prevalence of novel mutations in RBC cytoskeleton/enzyme genes. NGS has clinical utility and should be considered for accurate diagnosis. Further research into the molecular basis and genetic spectrum of HHA in the Hispanic population is needed.

Comparison of DNA Extraction Methods for the Detection of Canned Tuna Species with DNA Mini-Barcoding

Tuna is susceptible to species mislabeling due to its high demand, quick rate of production, and wide range of price points. DNA barcoding, a sequencing-based technique, allows for the detection of species mislabeling by targeting a standardized region of DNA. A mitochondrial control region (CR) DNA barcode has been found to be capable of species discrimination for tuna, but it is challenging to recover the entire DNA fragment from canned tuna. While a short fragment of CR, referred to as a “mini-barcode,” has shown some success with canned tuna species identification, more research is needed to improve identification rates. The objective of this study was to determine the optimal DNA extraction method for species identification of canned tuna using CR mini-barcoding. Four commercial DNA extraction kits were compared using a sample set of 24 different cans of tuna labeled as albacore, light tuna, skipjack, or yellowfin. All samples were tested in duplicate. The greatest success was found using the Qiagen DNeasy Blood and Tissue Kit and the Qiagen DNeasy Mericon Food Kit, which resulted in species identification for 42% of the samples. In comparison, the MP Biomedicals FastPrep-24 + Machery-Nagel NucleoSpin Tissue Kit resulted in species identification for 30% of the samples and the Qiagen DNeasy Blood and Tissue Kit + PowerClean Pro Cleanup Kit resulted in species identification for 21% of the samples. Overall, the top-performing DNA extraction methods for use with CR mini-barcoding of canned tuna products were determined to be the DNeasy Blood and Tissue Kit and the DNeasy Mericon Food Kit.