DNA PCR Research Articles

Evaluating serum electrolyte and trace element variations between Babesia ovis-infected and uninfected Lohi sheep

Babesiosis caused by Babesia ovis is a major threat to the livestock industry worldwide. In Pakistan, the Lohi sheep breed is an important economic resource, but limited information is available on the impact of B. ovis infection on this breed. This study aimed to investigate the serum electrolyte and trace element variations between B. ovis-infected and uninfected Lohi sheep from Pakistan. A total of 97 Lohi sheep was stratified based on the geographical distribution of Multan district, employing a multistage cluster sampling method. Blood and serum samples were collected from randomly selected sheep, and DNA extraction and PCR amplification were performed to detect B. ovis infection. Serum electrolyte and trace element levels were analyzed in infected (n=67) and uninfected (n=30) groups, stratified by age and gender. The study revealed a 69.07% overall infection rate of B. ovis in Lohi sheep. Infected sheep showed significantly elevated serum copper levels (p<0.0001), with no substantial differences observed in serum iron, sodium, potassium, and chloride levels. However, age-wise variance analysis revealed statistically significant variations in sodium and potassium levels (p<0.0001 and p<0.05, respectively). Notably, serum chloride levels differed between infected and uninfected females in individuals younger than two years (p<0.05). Serum iron levels remained consistent across different age groups. Comparative analysis indicated a higher prevalence of electrolyte imbalances, such as hyponatremia, hyperkalemia, hyperchloremia, and hypoferremia, in infected sheep compared to normal reference ranges, while instances of hypernatremia, hypokalemia, hypochloremia, and hyperferremia were less frequent. In conclusion, our study suggests that B. ovis infections could lead to alterations in serum electrolyte and trace element levels in Lohi sheep, emphasizing the importance of further research into the specific mechanisms driving these alterations to enhance disease management strategies tailored to this breed.

An efficient visual screening of gene knockout mutants in the insect pathogenic fungus Beauveria bassiana.

Beauveria bassiana is an entomopathognic fungus, which is widely employed in the biological control of pests. Gene disruption is a common method for studying the functions of genes involved in fungal development or its interactions with hosts. However, generating gene deletion mutants was a time-consuming work. The transcriptional factor OpS3 has been identified as a positive regulator of a red secondary metabolite oosporein in B. bassiana. In this study, we have designed a new screening system by integrating a constitutive OpS3 expression cassette outside one of the homologous arms of target gene. Ectopic transformants predominantly exhibit a red colour with oosporein production, while knockout mutants appear as white colonies due to the loss of the OpS3 expression cassette caused by recombinant events. This screening strategy was used to obtain the deletion mutants of both tenS and NRPS genes. Correct mutants were obtained by screening fewer than 10 mutants with a positive efficiency ranging from 50% to 75%. This system significantly reduces the workload associated with DNA extraction and PCR amplification, thereby enhancing the efficiency of obtaining correct transformants in B. bassiana.

Prevalence and genetic diversity of Anaplasma and Ehrlichia in ticks and domesticated animals in Suizhou County, Hubei Province, China

Anaplasma and Ehrlichia are tick-borne bacterial pathogens that cause anaplasmoses and ehrlichioses in humans and animals. In this study, we examined the prevalence of Anaplasma and Ehrlichia species in ticks and domesticated animals in Suizhou County, Hubei Province in the central China. We used PCR amplification and DNA sequencing of the 16S rRNA, groEL, and gltA genes to analyze. We collected 1900 ticks, including 1981 Haemaphysalis longicornis and 9 Rhipicephalus microplus, 159 blood samples of goats (n = 152), cattle (n = 4), and dogs (n = 3) from May to August of 2023. PCR products demonstrated that Anaplasma bovis, Anaplasma capra, and an Ehrlichia species were detected in the H. longicornis with the minimum infection rates (MIR) of 1.11%, 1.32%, and 0.05%, respectively; A. bovis, A. capra, and unnamed Anaplasma sp. were detected in goats with an infection rate of 26.31%, 1.31% and 1.97%, respectively. Anaplasma and Ehrlichia species were not detected from cattle, dogs and R. microplus ticks. The genetic differences in the groEL gene sequences of the Anaplasma in the current study were large, whereas the 16S rRNA and gltA gene sequences were less disparate. This study shows that ticks and goats in Suizhou County, Hubei Province carry multiple Anaplasma species and an Ehrlichia species, with relatively higher infection rate of A. bovis in goats. Our study indicates that multiple Anaplasma and Ehrlichia species exist in ticks and goats in the central China with potential to cause human infection.

Factors underlying the long-term efficacy of faecal microbiota transplantation for patients with irritable bowel syndrome

The long-term effects of the transplant dose, its administration route and repeated faecal microbiota transplantation (FMT) on the outcomes of FMT for patients with irritable bowel syndrome (IBS) are unknown. This study included 171 patients (125 females and 46 males): 90 g of donor feces was administered into the large intestine (LI) in 58, into the small intestine (SI) in 57, and into the SI twice (repeated SI) in 56. The patients provided a fecal sample and completed five questionnaires at the baseline and at 2 years after FMT. Fecal bacteria and the dysbiosis index were analyzed using 16S rRNA gene PCR DNA amplification/probe. The response rates at 2 years after FMT were 47.2%, 80.9%, and 76.6% in the LI, SI, and repeated-SI groups, respectively. The response rate was significantly higher in the SI and repeated SI groups than in the LI group. IBS symptoms at 2 years after FMT were less severe in the SI and repeated-SI groups than in the LI group. Fluorescent signals of several bacteria were significantly correlated with IBS symptoms and fatigue after FMT. No long-term adverse events were observed. In conclusion, administering the transplant to the SI increased the long-term response rate and reduced IBS symptom severity compared with administering it to the LI, and led to the long-term colonization of beneficial bacteria. There was no long-term difference between one and two FMT procedures (www.clinicaltrials.gov: NCT04236843).

The relationship between Toll-like receptor-4 genes and preeclampsia outcomes.

The study aimed to analyse the relationship of the rs4986790 locus of the TLR4 gene with the overall risk of preeclampsia, including both its early and late forms. The study used standard genetic analysis methods such as DNA extraction, PCR amplification, and genotyping of the rs4986790 locus of the TLR4 gene to assess the association with the development of preeclampsia and peripartal stroke in 207 pregnant women from the southern regions of Kazakhstan from 2016 to 2022, of whom 103 had peripartal stroke on the background of preeclampsia (the main group) and 104 preeclampsia (comparative group). The results of the study demonstrate that the AG and AG + GG genotypes at the rs4986790 locus of the TLR4 gene are significantly associated with an increased risk of developing an early form of preeclampsia. This opens up a new perspective in the identification of genetic markers that can serve as indicators of a tendency to develop preeclampsia in earlier periods of pregnancy. It was noted that the rs4986790 locus did not show a statistically significant association with the risk of late preeclampsia. An important aspect of the study revealed the relationship of genotypes with the development of peripartal stroke on the background of preeclampsia. This study offers practical insights for creating targeted genetic screening and personalised treatments for preeclampsia, aiming to improve patient outcomes. To fully understand the molecular mechanisms underlying the identified association, additional research is required to identify deeper molecular pathways and relationships, and to develop new strategies for the prevention and treatment of preeclampsia.

Evaluation of CMV DNA Antigenemia Status in Patients With Allogeneic Bone Marrow Transplant

Purpose: The risk of cytomegalovirus (CMV) reactivation following allogeneic hematopoietic stem cell transplantation (ASCT) reaches 30-50%, and there are numerous diagnostic tests to detect CMV replication. The most common tests used in this group of patients include 65kDa phosphoprotein (pp65) antigenemia immunofluorescence assay and nucleic-acid-based quantitative CMV-DNA polymerase chain reaction (qPCR). Material and Methods: In this study, patients who underwent ASCT and developed CMV positivity from 2009 to 2016 in our hospital were evaluated retrospectively. The study included samples of the same patient with antigenemia and CMV-DNA qPCR test for up to 48 hours. The study aimed to determine the factors affecting CMV DNA antigenemia and compare CMV DNA PCR and pp65 antigenemia immunofluorescence assay. Results: The results of 138 specimens of 39 patients who underwent ASCT were evaluated. The mean value of CMV PCR, which was positive for both tests, was 57.887 copies/ml (70- 1.213.633 copies/ml) and a significant correlation was found between the two tests and the positive samples (p = 0.018). The ROC analysis showed that 322 copies/ml CMV viral load in plasma corresponds to ≥1 antigen-positive cells/200 thousand leukocytes (Sensitivity: 68.5%; Specificity: 31.5%). CMV infection was observed in 32 samples; CMV DNA cut-off values of the reference according to CMV DNA PCR and antigenemia results, compared to the development of CMV infection, presented a significant correlation (p=0.004). Conclusion: Although there is a common agreement between antigenemia and CMV DNA PCR tests, one should keep in mind that the sensitivity of antigenemia test is low especially in the neutropenic period.

Oesophagostomum stephanostomum causing parasitic granulomas in wild chimpanzees (Pan troglodytes verus) of Taï National Park, Côte d'Ivoire.

Nematodes belonging to the genus Oesophagostomum frequently infect wild chimpanzees (Pan troglodytes) across widely separated field sites. Nodular lesions (granulomas) containing Oesophagostomum are commonly seen in the abdomen of infected chimpanzees post-mortem. At Taï National Park, Côte d'Ivoire, previous studies have identified larvae of a variety of Oesophagostomum spp. in wild chimpanzee stool, based on sequencing of larval DNA, and nodular lesions associated with Oesophagostomum, identified morphologically to the genus level but not sequenced. Here we present three recent cases of parasitic granulomas found post-mortem in chimpanzees at Taï. We complement descriptions of gross pathology, histopathology and parasitology with PCR and sequencing of DNA isolated from the parasitic nodules and from adult worms found inside the nodules. In all three cases, we identify Oesophagostomum stephanostomum as the causative agent. The sequences from this study were identical to the only other published sequences from nodules in nonhuman primates-those from the wild chimpanzees of Gombe, Tanzania.

Description of a 'plankton filtration bias' in sequencing-based bacterial community analysis and of an Arduino microcontroller-based flowmeter device that can help to resolve it.

Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.

In Utero Mother-to-Child Transmission of HIV-1 and the Associated Factors in Rwanda, Africa.

Mother-to-child transmission (MTCT) of HIV-1 and associated mortality continue to occur at unacceptably high rates, despite the extensive rollout and implementation of Prevention of Mother-to-Child Transmission (PMTCT) Programs, including the modified versions of Option B and B+ in 2010 and 2012, respectively. Maternal HIV viral load (VL) and socio-behavioral factors sustaining MTCT in Rwanda remain largely unexplored. The study examined the effects of socio-behavioral factors on maternal VL and their contribution to in utero transmission of HIV-1 in the context of Rwanda's HIV epidemic. A prospective cohort study was conducted in 862 mother-baby pairs enrolled in 10 PMTCT clinics in Rwanda. VL was determined on plasma and Dried Blood Spots samples, whereas HIV DNA PCR was performed to determine in utero MTCT of HIV of the babies immediately at birth and then at 3 weeks, 4 weeks, 6 months, and 18 months, together with HIV antibody testing to determine other forms of MTCT of HIV. Quantitative data on socio-behavioral factors were collected through a structured questionnaire. Linear regression and univariate analysis of variances using SPSS 25.0 were used to test the hypotheses. We found 22/862 (2.55%) cases of in utero transmission and a total of 32/862 (3.7%) cases of MTCT of HIV-1 over 18 study months. Maternal VL at delivery was significantly associated with the risk of in utero transmission of HIV-1. Socio-behavioral factors associated with elevated maternal VL at delivery included alcohol, smoking, multiple sexual partners, mothers' income, being a casual laborer, and distance to health care services. We report an MTCT rate of 3.7% in our study population over the 18 months, higher than the national average of 1.5%, the majority of which occurred in utero. MTCT cases were attributable to failure to suppress maternal VL.

First Report of Tetranychus truncatus Ehara (Acari: Tetranychidae) Infesting Groundnut (Arachis hypogaea L.) in India through Morphological and Molecular Insight

Background: Red spider mite, Tetranychus truncatus Ehara (Acari: Tetranychidae) infests many agriculture and horticulture crops in India, but to date it had not been found damaging cultivated groundnut. During 2022-23, the incidence of this species was high in many groundnut growing regions of Tamil Nadu. Identification of the species is highly essential for effective management of the particular pest. Hence, the aim of this research was to identify the mite species infesting groundnut crop and describe the damage caused. Methods: Survey was carried out all over Tamil Nadu and samples of mite infested groundnut leaves were collected from field based on damage symptoms, observed and examined under Stereo zoom microscope, microslides were prepared using Hoyer’s medium and taxonomic characters were studied under phase contrast microscope. Molecular analysis was done by genomic DNA isolation, PCR amplification, sequencing and BLAST performed to check the identity with GenBank Sequences. ITS2 primer was used. Result: Red spider mite species, T. truncatus was identified first time in groundnut through both morphological characters and molecular tools. Female: Idiosomal setae longer than the interval between their longitudinal bases and gradually tapers distally. Diamond- shaped pattern of striae between e1 and f1 setal bases. Tarsus I with 4 tactile setae proximal to proximal duplex setae. Male: Aedeagus with tiny terminal knob, apparently truncate with a slight indentation on the dorsal margin.

Multiplex PCR specific for genus Phytophthora and P. nicotianae with an internal plant DNA control for effective quarantine of Phytophthora species in Japan

To prevent threats from pathogens such as Phytophthora species from international plant trade, molecular identification techniques are needed for rapid, accurate quarantine inspection. Here, for quarantine control in Japan, we developed a simple DNA extraction for plants and a practical detection method that combines multiplexed PCR using primers specific for Phytophthora species, for P. nicotianae, which is the only non-quarantine Phytophthora species, and as internal controls, for plants. For the new genus-level primer set, we modified previously reported genus-specific primers to improve detectability. The new primers were able to detect mycelial DNA of 155 taxa among Phytophthora clades 1–10, with a sensitivity of 100 fg/µL for three representative species, P. ramorum, P. kernoviae and P. nicotianae. In the PCRs using DNA from non-target species, amplification was observed for only three taxa, and for some strains, four taxa in a closely related genus. Duplex and triplex PCR of the genus-specific primers combined with previously reported plant primers verified the success of DNA extraction and PCR detection from diseased plant samples, and in the triplex PCR, whether the pathogen was diagnosed as P. nicotianae or not by the species-specific primer. The new method detected the pathogen in naturally infected and inoculated plants. The amplicons using the genus-specific primer have enough variation to be sequenced to identify the species. This new method can be used immediately for detecting Phytophthora species and for quarantine control in Japan.

Molecular authentication of commercial "Qian-hu" through the integration of nrDNA internal transcribed spacer 2 and nucleotide signature.

Peucedani Radix, also known as "Qian-hu" is a traditional Chinese medicine derived from Peucedanum praeruptorum Dunn. It is widely utilized for treating wind-heat colds and coughs accompanied by excessive phlegm. However, due to morphological similarities, limited resources, and heightened market demand, numerous substitutes and adulterants of Peucedani Radix have emerged within the herbal medicine market. Moreover, Peucedani Radix is typically dried and sliced for sale, rendering traditional identification methods challenging. We initially examined and compared 104 commercial "Qian-hu" samples from various Chinese medicinal markets and 44 species representing genuine, adulterants or substitutes, utilizing the mini barcode ITS2 region to elucidate the botanical origins of the commercial "Qian-hu". The nucleotide signature specific to Peucedani Radix was subsequently developed by analyzing the polymorphic sites within the aligned ITS2 sequences. The results demonstrated a success rate of 100% and 93.3% for DNA extraction and PCR amplification, respectively. Forty-five samples were authentic "Qian-hu", while the remaining samples were all adulterants, originating from nine distinct species. Peucedani Radix, its substitutes, and adulterants were successfully identified based on the neighbor-joining tree. The 24-bp nucleotide signature (5'-ATTGTCGTACGAATCCTCGTCGTC-3') revealed distinct differences between Peucedani Radix and its common substitutes and adulterants. The newly designed specific primers (PR-F/PR-R) can amplify the nucleotide signature region from commercial samples and processed materials with severe DNA degradation. We advocate for the utilization of ITS2 and nucleotide signature for the rapid and precise identification of herbal medicines and their adulterants to regulate the Chinese herbal medicine industry.

Differential Effect of 2 Hormonal Contraceptives on the Relative Telomere Length of Youth With Type 1 Diabetes.

Adolescents and young women (AYA) with type 1 diabetes (T1D) may require hormonal contraception for an extended period. However, it is unclear what effect hormonal contraception has on telomere length, a marker of the risk for complications. To investigate the relative telomere length (RTL) in AYA with T1D (AYA-T1D) and healthy young women (AYA-C) after 18 months of combined oral contraception use (COC) with ethinyl estradiol/desogestrel, or a subdermal etonogestrel implant (IM). A nonrandomized prospective study was performed in which 39 AYA-T1D and 40 AYA-C chose the COC or the IM. RTL was measured by monochrome multiplex-quantitative PCR in DNA from peripheral blood mononuclear cells (PBMC). The impact of contraceptives and clinical variables on RTL was assessed using lineal regression analysis. Longer RTL compared to baseline was observed in AYA-T1D (P < .05) and AYA-C (P < .01) after using the IM. However, the total of AYA and the AYA-C group treated with COC decreased RTL after 18 months of treatment compared to baseline (P < .05). The type of contraceptive used was determinant for the changes in RTL compared to baseline in all subjects and controls (P ≤ .006). For AYA-T1D, HbA1c levels were not associated with RTL, but the high-sensitivity C-reactive protein was negatively related with the changes in RTL at 18 months compared to baseline (standardized R2 : 0.230, P = .003). IM was associated with longer RTL in AYA-T1D and AYA-C. In contrast, a shortening of telomere length in PBMC was observed after using COC.

An Evaluation of High-Risk HPV in Squamous Cell Carcinomas of the Lip in a South African Cohort

BackgroundTo determine the prevalence of HR-HPV in a series of lip SCC from South African patients, using currently accepted HPV-testing methodologies and to define the clinical and histomorphologic features of HPV-associated lip SCC.MethodsFifty SCC of lip and 50 control cases were tested for HR-HPV using p16 and HR-HPV DNA PCR. p16-equivocal/positive and HPV DNA PCR-positive SCC were further evaluated for the expression of HPV-16 and HPV-18 mRNA transcripts using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to confirm transcriptionally active HPV.Resultsp16 was positive in 22% (n = 11) and equivocal in 4% (n = 2) of the SCC. One p16-positive case showed positivity for both HPV-16 DNA and HPV-16 E6/E7 mRNA transcripts (HPV prevalence rate of 2%). The HPV-positive case was non-keratinizing and occurred in an 80-year-old female. The two p16-equivocal cases were HR-HPV DNA positive and mRNA PCR negative. p16 was found to have a positive predictive value of 9%.ConclusionFindings from our cohort of lip SCC suggest that HR-HPV may have an insignificant role in the pathogenesis of SCC at this site. Due to its low ppv, p16 is insufficient to establish HR-HPV infection in SCC of the lip. The combination of p16 and DNA PCR appears to correlate with the presence of transcriptionally active virus. HPV E6/E7 mRNA detection is the gold standard for identifying HR-HPV. mRNA testing is not widely available in sub-Saharan Africa due to technical and financial constraints; however, the test appears to be of great value in p16-equivocal lip SCC.

Antibiotic Resistant and Plasmid Borne Bacteria Associated with Locally Produced Honey in Enugu State, Nigeria

Aim: The aim of this study is to isolate and identify bacteria contaminants present in the honey samples sold in Ogbete market and detect the presence of imipenem resistance genes in the isolates. Place and Duration of Study: A total of four samples were collected from Ogbete market at Zenith bank, Peace mass, Wheelbarrow and Peace park stations between the early hours of the morning (8-9am) within the month of April, 2023. Methodology: Microbiological analysis was carried out on the samples, including antimicrobial susceptibility test using disc diffusion method., after which Molecular analysis involving DNA extraction, PCR and Plasmid Profiling, were carried out. Results: The total mean heterotrophic bacterial count ranged from 0.03±2.5×103cfu/ml to 22.1±25.5×103cfu/ml. The highest total mean heterotrophic bacterial count was recorded in Zenith bank while the lowest was in Peace mass. The bacteria isolated and characterized through morphological and biochemical tests include Escherichia coli (45%) Klebsiella spp. (41%), Staphylococcus spp. (9%) and Streptococcus spp. (5%). Escherichia coli had the highest frequency of occurrence at 45% while Streptococcus spp. had the lowest at 5%. The sensitivity test showed that the isolates with the highest frequency of occurrence, Escherichia coli and Klebsiella spp. posed a high resistance to Imipenem and Nalidixic at 80% while the least resistance was in Levofloxacin at 10% from these two isolates. The gene of interest, BlaIMP was found after PCR assay. Plasmid DNA was further carried out using the alkaline lysis method using the Zymo research kit. All isolates possessed a single plasmid with molecular weight of 23.1kbp. Conclusion: These isolates may undergo horizontal gene transfer and confer resistance to other microorganisms. Thus, there is need for the development of proper measures to counter bacterial contamination of locally produced honey as this poses a threat to public health.

A Study of Genotypic Characterization of ESBL and MBL Genes of β-Lactamase Producing Pseudomonas aeruginosa in Various Clinical Samples

Pseudomonas aeruginosa, a Gram-negative bacterium, presents a substantial challenge in healthcare due to its adaptability and resistance. This study delves into its genotypic characteristics, focusing on ESBL and MBL genes. The prevalence of P. aeruginosa in nosocomial infections, the research aims to decipher resistance mechanisms crucial for tailored interventions. The study includes 170 non-repetitive clinical samples with protocols. Antibiotic susceptibility testing reveals diverse resistance patterns. Molecular detection of ESBL and MBL genes involves DNA isolation, PCR amplification, and gel electrophoresis. The study examined 170 P. aeruginosa samples, revealing gender-specific variations with 65.91% male and 34.09% female isolates. Antimicrobial testing displayed resistance in Ceftazidime (59%) and Ciprofloxacin (48%), while Ticarcillin-clavulanic acid showed promising sensitivity (58%). Molecular identification unveiled diverse resistance genes across sample types, emphasizing genetic complexity. The study underscores the urgency for targeted therapeutic interventions and novel antimicrobial strategies against P. aeruginosa infections. As antimicrobial resistance complexities persist, this research guides efforts toward a profound understanding of clinical interventions and strategic antimicrobial management.

Identification of a new mutation in the ACTL9 gene in men with unexplained infertility.

Infertility is defined as the failure to achieve pregnancy after one year of unprotected intercourse within a marital relationship. Approximately 10%-15% of couples worldwide experience infertility issues, with nearly half of these cases attributed to male factors. Among men with unexplained infertility, genetic mutations have been identified as a potential cause. Studies have indicated that mutations affecting the function of the protein encoded by the ACTL9 gene may play a role in male infertility. The purpose of this research was to identify mutations in the ACTL9 gene associated with male infertility in a sample of 40 infertile men with unknown causes. Genomic DNA extraction and PCR amplification were carried out on samples from each individual. The genetic material was then analyzed using Sanger sequencing, followed by bioinformatics and segregation analysis to determine the potential effects of the observed variations. A novel genetic variant, c.376G>A (p.Glu126Lys), was identified in an infertile male individual, representing a previously unreported finding that was validated through segregation analyses. This specific variant induces a change from glutamate to lysine at the amino acid level by replacing the nucleotide G with A in the genomic DNA sequence, consequently impacting the secondary structure and function of the protein. The conclusive analysis of the procedure indicated that this alteration has the potential to interfere with the process of fertilization, ultimately resulting in the complete failure of fertilization (TFF) and causing male infertility.

Isolation and Identification of Nematode-Infecting Microsporidia.

Nematodes are naturally infected by the fungal-related pathogen microsporidia. These ubiquitous eukaryotic parasites are poorly understood, despite infecting most types of animals. Identifying novel species of microsporidia and studying them in an animal model can expedite our understanding of their infection biology and evolution. Nematodes present an excellent avenue for pursuing such work, as they are abundant in the environment and many species are easily culturable in the laboratory. The protocols presented here describe how to isolate bacterivorous nematodes from rotting substrates, screen them for microsporidia infection, and molecularly identify the nematode and microsporidia species. Additionally, we detail how to remove environmental contaminants and generate a spore preparation of microsporidia from infected samples. We also discuss potential pitfalls and provide suggestions on how to mitigate them. These protocols allow for the identification of novel microsporidia species, which can serve as an excellent starting point for genomic analysis, determination of host specificity, and infection characterization. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Gathering samples Support Protocol 1: Generating 10× and 40× Escherichia coli OP50 and seeding NGM plates Basic Protocol 2: Microsporidia screening, testing for Caenorhabditis elegans susceptibility, and sample freezing Basic Protocol 3: DNA extraction, PCR amplification, and sequencing to identify nematode and microsporidia species Basic Protocol 4: Removal of contaminating microbes and preparation of microsporidia spores Support Protocol 2: Bleach-synchronizing nematodes.

Establishment of Transgene-Free Porcine Induced Pluripotent Stem Cells.

Although protocols to generate authentic transgene-free mouse and human induced pluripotent stem cells (iPSCs) are now well established, standard methods for reprogramming porcine somatic cells still suffer from low efficiency and transgene retention. The Basic Protocol describes reprogramming procedures to establish transgene-free porcine iPSCs (PiPSCs) from porcine fibroblasts. This method uses episomal plasmids encoding POU5F1, SOX2, NANOG, KLF4, SV40LT, c-MYC, LIN28A, and microRNA-302/367, combined with an optimized medium, to establish PiPSC lines. Support protocols describe the establishment and characterization of clonal PiPSC lines, as well as the preparation of feeder cells and EBNA1 mRNA. This optimized, step-by-step approach tailored to this species enables the efficient derivation of PiPSCs in ∼4 weeks. The establishment of transgene-free PiPSCs provides a new and valuable model for studies of larger mammalian species' development, disease, and regenerative biology. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Reprogramming of porcine fibroblasts with episomal plasmids Support Protocol 1: Preparation of mouse embryonic fibroblasts for feeder layer Support Protocol 2: Preparation of in vitro-transcribed EBNA1 mRNA Support Protocol 3: Establishment of clonal porcine induced pluripotent stem cell (PiPSC) lines Support Protocol 4: PiPSC characterization: Genomic DNA PCR and RT-PCR Support Protocol 5: PiPSC characterization: Immunostaining.

BIOCHAR IMPROVES TOMATOES GROWTH CHALLENGED WITH KHOKHRAN VIRUS INFECTION

Tomato production in Pakistan is being seriously hampered by begomoviruses. To sustain tomato production and to contribute the growing economy of Pakistan, the researchers should focus on the innovative and organic disease prevention/management options. In this regard, the utilization of biochar as a soil amendment and to activate the defense mechanism of plants against invading pathogens emerged to be a reasonable solution. In this study, biochar produced from available organic waste through pyrolysis was used to tackle the begomovirus called the Khokhran virus. Various levels of biochar were applied alongside the soil. Five treatments were used, each involving the addition of biochar to soil: only soil with no biochar served as control, then treatments with 5 and 10% Green Biochar each, as well as 5 and 10% Wood Biochar amended soil substrate. According to the results of root and shoot mass, the treatment with 5%, Green Biochar yielded the best outcome. Plants grown with Green Biochar were taller and had higher yields compared to those in other treatments. Additionally, tests including PCR assays, RNA extraction, and DNA quantification were conducted to confirm the presence of viral load in each treatment. In conclusion, 5% Green Biochar was found to be most effective against the Khokhran virus, by boosting plant growth and inducing resistance.