Nanopore sequencing in distinguishing between wild-type and vaccine strains of Varicella-Zoster virus

BACKGROUND

The introduction of varicella vaccines into routine pediatric immunization programs has led to a considerable reduction in varicella incidence. However, there have been reports of varicella, herpes zoster, and meningitis caused by the vaccine strain of varicella-zoster virus (VZV), raising concerns. Establishing the relationship between the wild-type and vaccine strains in VZV infections among previously vaccinated individuals is crucial. Differences in the single nucleotide polymorphisms (SNPs) among vaccine strains can be utilized to identify the strain. In this study, we employed nanopore sequencing to identify VZV strains and analyzed clinical samples.

METHODS

We retrospectively examined vesicle and cerebrospinal fluid samples from patients with VZV infections. One sample each of the wild-type and vaccine strains, previously identified using allelic discrimination real-time PCR and direct sequencing, served as controls. Ten samples with undetermined VZV strains were included. After DNA extraction, a long PCR targeting the VZV ORF62 region was executed. Nanopore sequencing identified SNPs, allowing discrimination between the vaccine and wild-type strains.

RESULTS

Nanopore sequencing confirmed SNPs at previously reported sites (105,705, 106,262, 107,136, and 107,252), aiding in distinguishing between wild-type and vaccine strains. Among the ten unknown samples, nine were characterized as wild strains and one as a vaccine strain. Even in samples with low VZV DNA levels, nanopore sequencing was effective in strain identification.

CONCLUSION

This study validates that nanopore sequencing is a reliable method for differentiating between the wild-type and vaccine strains of VZV. Its ability to produce long-read sequences is remarkable, allowing simultaneous confirmation of known SNPs and the detection of new mutations. Nanopore sequencing can serve as a valuable tool for the swift and precise identification of wild-type and vaccine strains and has potential applications in future VZV surveillance.

Association between miR-202, miR-211, and miR-1238 gene polymorphisms and risk of vitiligo

Vitiligo, as a common pigment defect in the skin, hair, and mucous membranes, results from the destruction of melanocytes. Recent investigations have shown that miRNA dysregulation contributes in the pathogenesis of vitiligo. Therefore, in this research, our aim is to explore the relationship between miR-202 rs12355840, miR-211 rs8039189, and miR-1238 rs12973308 polymorphisms and susceptibility to vitiligo. A total number of 136 vitiligo patients and 129 healthy individuals as a control group were included in this research. The salting out approach was implemented to extraction genomic DNA. The genetic polymorphisms of miR-202 rs12355840, miR-211 rs8039189, and miR-1238 rs12973308 were determined using PCR-RFLP approach. The findings revealed that miR-202 rs12355840 polymorphism under codominant (CT and TT genotypes), dominant, recessive, overdominant, and also allelic models is correlated with increased risk of vitiligo. In addition, codominant, dominant, overdominant, as well as allelic models of miR-211 rs8039189 polymorphism decrease risk of vitiligo. No significant relationship was observed between the miR-1238 rs12973308 polymorphism and susceptibility to vitiligo. The miR-211 rs8039189 polymorphism may serve a protective effect on vitiligo development and miR-202 rs12355840 polymorphism may act as a risk factor for vitiligo susceptibility.

Epidemiological survey, molecular profiling and phylogenetic analysis of cutaneous leishmaniasis in Khyber Pakhtunkhwa, Pakistan

BACKGROUND

Cutaneous leishmaniasis (CL), an emerging vector-borne ailment in Khyber Pakhtunkhwa (KPK), Pakistan, exhibits diverse spread patterns and outbreaks.

METHODS

To comprehend its epidemiology and identify parasite species, we conducted an active survey on suspected CL cases (n=8845) in KPK.

RESULTS

Microscopy and internal transcribed spacer-1 PCR-restriction fragment length polymorphism (RFLP) molecular techniques detected Leishmania spp. in blood samples. Phylogenetic analysis gauged genetic affinities with other areas. District Bannu displayed the highest CL impact (14.58%), while Swat had the lowest impact (4.33%) among cases. Annual blood examination rate, parasite incidence and slide positivity rate were 4.96 per 1000 people, 0.0233 and 0.047%, respectively. CL infections were prevalent in 1- to 20-y-olds, with males (57.17%) more vulnerable than females (42.82%). Single lesions occurred in 43.73% of patients, while 31.2% people had two lesions, 17.31% had three lesions and 7.74% had more than three lesions. Most had sand-fly exposure but lacked preventive measures like repellents and bed nets. Leishmania tropica was confirmed via RFLP analysis in amplified samples. Phylogenetic analysis unveiled genetic parallels between L. tropica of KPK and isolates from China, Iran, Afghanistan, India, Syria and Morocco.

CONCLUSIONS

Urgent comprehensive control measures are imperative. Early detection, targeted interventions and raising awareness of CL and sand-fly vectors are vital for reducing the disease's impact. International collaboration and monitoring are crucial to tackle Leishmania spp.'s genetic diversity and curtail its cross-border spread.

Detection of Toxoplasma gondii and Sarcocystis sp. in the meat of common minke whale (Balaenoptera acutorostrata): A case of suspected food poisoning in Japan

A case of suspected food poisoning related to the consumption of raw meat from a common minke whale (Balaenoptera acutorostrata) was reported in Tokyo, Japan, in June 2020. Microscopic analysis revealed tissue cysts of Toxoplasma gondii and sarcocysts of Sarcocystis sp. in whale meat. The SAG2 and ITS1 region sequences of T. gondii were detected in the DNA extracted from the meat. Genotyping of the multilocus nested PCR-RFLP using the genetic markers SAG1, SAG2 (5'- SAG2, 3'-SAG2, and alt. SAG2), SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico revealed that the genotype of T. gondii was type II, with a type I pattern for the L358 locus. In the phylogenetic analyses of the six loci (GRA6, GRA7, SAG1, HP2, UPRT1, and UPRT7), these sequences clustered into haplogroup 2. Moreover, the sequences of the virulence-related genes ROP5 and ROP18 of T. gondii isolated from whale meat were similar to those of the type II ME49 reference strain. Sequence analyses of the mtDNA cox1 gene, 18S rRNA gene, and ITS1 region indicated the highest similarity of sarcocyst isolated from whale meat to Sarcocystis species that infect birds or carnivores as intermediate hosts; however, the species could not be identified. To our knowledge, this is the first report of T. gondii and Sarcocystis spp. being detected in same whale meat ingested by patients involved in a suspected food poisoning case in Japan.

Finger printing-RFLP analysis of chromosomal IS6110 insertion sequence and PCR diagnosis of pulmonary tuberculosis, isolated from patients in El Hajeb region of Morocco

Tuberculosis (TB) is one of the contagious diseases caused by M. tuberculosis (MTB) bacteria. Prompt diagnosis is one of the active solutions to control the spread of this infection. Besides, a targeted, specific and non-complex diagnosis can prove promising in this type of epidemic. This study was designed to compare the efficiencies of a diagnosis by Ziehl-Neelsen staining (ZN) and by the polymerase chain reaction (PCR) technique. Samples presented smear-positive pulmonary TB were subjected to Chromosomal restriction fragment length polymorphism of IS6110 (IS6110-RFLP) for fingerprinting profile determination. The results showed that out of 100 sputum samples of suspected case, 53 were positive. Numbers of positive individuals for tuberculosis obtained by the different diagnostic techniques, to know, (ZN staining; culture and PCR) were respectively: 6, 25 and 22. Chromosomal RFLP fingerprinting profile revealed the presence of five different genotypes obtained from seven tested isolates. These results suggest that molecular techniques are alternative tool for fast and specific diagnosis of pulmonary MTB from sputum.

Effect of MAOA rs1465108 polymorphism on susceptibility to substance/alcohol use disorder: a novel PCR-RFLP assay for the detection of MAOA rs1465108

BACKGROUND

The health and social consequences of substance/alcohol use disorders are harmful. Most of the individuals cannot stop using them due to more likely their genetic background. The current study aimed both to develop a novel PCR-RFLP method for genotyping of MAOA rs1465108 and to analyze the effect of MAOA rs1465108 on the risk of alcohol (AUD), opioid (OUD) or methamphetamine (MUD) use disorders and on the depressive and anxiety symptoms in a Turkish population.

METHODS AND RESULTS

A total of 353 individual with AUD (n = 154), OUD (n = 160) or MUD (n = 39) and 109 healthy subjects were included. The intensity of anxiety and depressive symptoms and craving and opioid withdrawal were measured by appropriate scales. Logistic regression analysis revealed no association between MAOA rs1465108 polymorphism and substance/alcohol use disorder (p > 0.05). Healthy subjects (3.0) had significantly lower levels of depressive symptoms than individuals with OUD (27.0), AUD (21.0) and MUD (25.5) groups. The severity of depressive symptoms was significantly higher in OUD as compared to AUD. There was a statistically significant difference between individuals with AUD, OUD and MUD in view of the average ages of first use (17, 19 and 20 years, respectively) (p < 0.05).

CONCLUSIONS

The results presented here do not support the hypothesis that MAOA rs1465108 is associated with substance/alcohol use disorders. The intensity of depressive symptoms could be changed according to the abused substance type. A novel PCR-RFLP was developed for genotyping of MAOA rs1465108 polymorphism, which could be a better option for laboratories without high technology equipment.

Droplet digital polymerase chain reaction to measure heteroplasmic m.3243A>G mitochondrial mutations

OBJECTIVE

Different mitochondrial DNA genotypes can coexist in a cell population as well as in a single cell, a condition known as heteroplasmy. Here, we accurately determined the heteroplasmy levels of the m.3243A>G mutation, which is the most frequently identified mutation in patients with mitochondrial diseases, using droplet digital polymerase chain reaction (ddPCR).

METHODS

The m.3243A>G heteroplasmy levels in artificial heteroplasmy controls mixed with various proportions of wild-type and mutant plasmids were measured using ddPCR, PCR-restriction fragment length polymorphism, and Sanger sequencing. The m.3243A>G heteroplasmy levels in DNA, extracted from the peripheral blood of patients with suspected mitochondrial disease and healthy subjects, were determined using ddPCR.

RESULTS

The accuracy of the ddPCR method was high. The lower limit of detection was 0.1%, which indicated its higher sensitivity compared with other methods. The m.3243A>G heteroplasmy levels in peripheral blood, measured using ddPCR, correlated inversely with age at the time of analysis. The m.3243A>G mutation may be overlooked in the peripheral blood-derived DNA of elderly people, as patients >60 years of age have heteroplasmy levels <10%, which is difficult to detect using methods other than the highly sensitive ddPCR.

CONCLUSION

ddPCR may be considered an accurate and sensitive method for measuring m.3243 A>G heteroplasmy levels of mitochondrial DNA.

Mutagenic primer-based novel multiplex PCR-RFLP technique to genotype BECN1 SNPs rs10512488 and rs11552192

BACKGROUND

Single Nucleotide Polymorphisms (SNPs) in candidate autophagy gene BECN1 could influence its functions thereby autophagy process. BECN1 noncoding SNPs were found to be significantly associated with neurodegenerative disease and type 2 diabetes mellitus. This study aimed to develop a simultaneous genotyping technique for two BECN1 SNPs (rs10512488 and rs11552192).

METHODS

A mutagenic primer-based approach was used to introduce a NdeI restriction site to genotype rs10512488 by Artificial-Restriction Fragment Length Polymorphism (A-RFLP) along with rs11552192 by Polymerase Chain Reaction (PCR)-RFLP. Multiplexing PCR and restriction digestion reactions were set up for simultaneous genotyping of both SNPs in 100 healthy individuals. Genotypic and allele frequencies were manually calculated, and the Hardy-Weinberg Equilibrium was assessed using the chi-square test.

RESULTS

We successfully developed PCR and RFLP conditions for the amplification and restriction digestion of both SNPs within the same tube for genotyping. The results of genotyping by newly developed multiplexing PCR-RFLP technique were concordant with the genotypes obtained by Sanger sequencing of samples. Allelic frequencies of rs10512488 obtained were 0.15 (A) and 0.85 (G), whereas allelic frequencies of rs11552192 were 0.16 (T) and 0.84 (A).

CONCLUSION

The newly developed technique is rapid, cost-effective and time-saving for large-scale applications compared to sequencing methods and would play an important role in low-income settings. For the first time, allelic frequencies of rs10512488 and rs11552192 were reported among the North Indian population.

Leiomyoma and the importance of genetic variation on genes related to the vasculature system - CβS, MTHFR, NOS3, CYBA, and ACE1

OBJECTIVE

The link between the systemic vasculature system and tumor biology is here investigated by studying the contribution of CβS (844ins68), MTHFR (677C > T), NOS3 (4a/4b), CYBA (C242T), and ACE1 (I/D) genes to leiomyoma onset, uterus and leiomyoma volumes.

METHODS

DNA samples from 130 women with leiomyomas and 527 from healthy women were genotyped by PCR or PCR-RFLP. Qui-square (χ2) or Fisher's exact test were used to test associations. All the mentioned tests were performed in IBM® SPSS® Statistics Version 28. Statistical significance was defined as a p-value < 0.05.

RESULTS

Results revealed that CβS (in the codominant and allelic models, p = 0.044 and, p = 0.015, OR = 1.791 [1.114-2.879], respectively), MTHFR (in the codominant, allelic and dominant models, p = 0.009, p = 0.002, OR = 0.585 [0.416-0.824] and p = 0.003, OR = 0.527 [0.346-0.802], respectively) and ACE1 (dominant model, p = 0.045, OR = 0.639 [0.411-0.992]) genes are associated with leiomyoma onset. NOS3 4a4a genotype is associated with a lower uterus volume (p = 0.004). This study also uncovers intriguing epistatic interactions among some genes that further accentuate their roles in disease modulation. Indeed, the epistatic interactions between the CC genotype (MTHFR) and (+/+) (CβS; p = 0.003), 4b4b (NOS3; p = 0.006, OR = 2.050 [1.223-3.439]) or DD (ACE1; p < 0.001, OR = 2.362 [1.438-3.880]) were shown to be associated with the disease, while 4a presence (NOS3) in epistasis with I presence (ACE1), increased the effect protection having just the I allele presence (p = 0.029, OR = 0.446 [0.214-0.930]).

CONCLUSIONS

We conclude that variation in genes related to the systemic vascular system can play a role in the onset and development of leiomyoma.

[Identification of Cervi Cornu (Cervus elaphus) and its formula granules based on PCR-RFLP]

Cervi Cornu is the ossified antler, or the base antler that falls off in the spring of the following year after the pilose antler is sawn off from Cervus elaphus or C. nippon, as a precious traditional Chinese medicine, has been recognized for its medicinal value and widely used in clinical practice. However, the origins of Cervi Cornu are miscellaneous, and Cervi Cornu is even mixed with adulterants in the market. Currently, there is a shortage of ways to identify Cervi Cornu and no standard to control the quality of Cervi Cornu. So it is valuable to develop a way to effectively identify Cervi Cornu from the adulterants. In this study, the differences in the mitochondrial barcode cytochrome b(Cytb) gene sequences of C. elaphus, C. nippon and their related species were compared and the specific single nucleotide polymorphism(SNP) sites on the Cytb sequences of Cervi Cornu were screened out. According to the screened SNPs, Cervi Cornu-specific primers dishmy-F and dishmy-R were designed. The PCR system was established and optimized, and the tolerance and feasibility of Taq polymerases and PCR systems affecting the repeatability of the PCR method were investigated. The amplification products of C. elaphus and C. nippon were digested using the restriction enzyme MseⅠ. The results showed that after electrophoresis of the product from PCR with the annealing temperature of 56 ℃ and 35 cycles, a single specific band at about 100 bp was observed for C. elaphus samples, and the product of C. elaphus samples was 60 bp shorter than that of C. nippon samples. There was no band for adulterants from other similar species such as Alces alces, Rangifer tarandus, Odocoileus virginianus, O. hemionus, Cap-reolus pygargus, Przewalskium albirostis and negative controls. The polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP) method established in this study can quickly and accurately identify Cervi Cornu originated from C. elaphus in crude drugs, standard decoctions, and formula granules, and distinguish the origins of Cervi Cornu products, i.e., C. nippon and similar species. This study can be a reference for other studies on the quality standard of other formula granules of traditional Chinese medicines.

Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method

PURPOSE

A new high-resolution next-generation sequencing (NGS)-based method was established to type closely related European type II Toxoplasma gondii strains.

METHODS

T. gondii field isolates were collected from different parts of Europe and assessed by whole genome sequencing (WGS). In comparison to ME49 (a type II reference strain), highly polymorphic regions (HPRs) were identified, showing a considerable number of single nucleotide polymorphisms (SNPs). After confirmation by Sanger sequencing, 18 HPRs were used to design a primer panel for multiplex PCR to establish a multilocus Ion AmpliSeq typing method. Toxoplasma gondii isolates and T. gondii present in clinical samples were typed with the new method. The sensitivity of the method was tested with serially diluted reference DNA samples.

RESULTS

Among type II specimens, the method could differentiate the same number of haplotypes as the reference standard, microsatellite (MS) typing. Passages of the same isolates and specimens originating from abortion outbreaks were identified as identical. In addition, seven different genotypes, two atypical and two recombinant specimens were clearly distinguished from each other by the method. Furthermore, almost all SNPs detected by the Ion AmpliSeq method corresponded to those expected based on WGS. By testing serially diluted DNA samples, the method exhibited a similar analytical sensitivity as MS typing.

CONCLUSION

The new method can distinguish different T. gondii genotypes and detect intra-genotype variability among European type II T. gondii strains. Furthermore, with WGS data additional target regions can be added to the method to potentially increase typing resolution.

ATR1 A1166C (rs5186), FII G20210A (rs1799963), FV G1691A (rs6025), FXIII 97G > T (rs11466016) and MTHFR A1298C (rs1801131) polymorphisms and the risk of ST-elevation myocardial infarction in young Mexican individuals

BACKGROUND

Previous studies had identified genetic variants associated with Myocardial Infarction, but results are inconclusive. We examined the association between FII G20210A (rs1799963), FV G1691A (rs6025), FXIII 97G > T (rs11466016), ATR1 A1166C (rs5186) and MTHFR A1298C (rs1801131) polymorphisms and ST elevation Myocardial Infarction in young Mexican individuals.

METHODS

We included a total of 350 patients with Myocardial Infarction <45 years old and 350 controls matched by age and gender. The polymorphisms were analyzed by PCR-RFLP using specific restriction enzymes. DNA fragments were separated by electrophoresis in 2% gel of agarose and visualized using SYBR green.

RESULTS

The A1166C (p = 0.004) but not FXIII 97G > T (p = 0.19), G20210A (p = 0.32), G1691A (p = No significant) and A1298C (p = 0.21) polymorphisms were associated with increased risk for ST elevation Myocardial Infarction. Moreover, dyslipidemia, hypertension, smoking and family history of atherothrombotic disease were associated.

CONCLUSIONS

We found that A1166C represented increased risk for ST elevation Myocardial Infarction. However, G20210A, G1691A, 97G > T, and A1298C were not associated. In addition, we had determined that Glu298Asp, PLA1/A2, TAFI Thr325Ile, ACE I/D, AGT M235T and PAI-1 4G/5G polymorphisms represented increased risk in the same group of patients. However, MTHFR C677T, AGT T174M, FV G1691A, TSP-1 N700S, MTHFR C677T and TAFI 174 M polymorphisms were no associated. Our results suggest that in young patients with ST Myocardial Infarction, those polymorphisms could contribute to premature endothelial dysfunction, atherothrombosis, vasoconstriction, increased platelet aggregation, muscle cell migration and proliferation. Further studies are required to try to better assess gene-gene and gene-modifiable factors interaction.

Detection of Internal Transcribed Spacer 1 and hsp70 Genetic Markers Using Restriction Fragment Length Polymorphisms and Sequencing in Identification of Leishmania Species Causing Tegumentary Leishmaniasis in Brazil

The identification of Leishmania species that cause tegumentary leishmaniasis (TL) is important for taxonomic and prognostic purposes. Molecular analysis using different Leishmania genomic targets is the most useful method for identifying Leishmania species. Therefore, we evaluated the performance of ribosomal RNA internal transcribed spacer 1 (ITS1) and heat shock protein (hsp70) genetic markers by polymerase chain reaction (PCR), followed by restriction fragment length polymorphism analysis (RFLP) and sequencing, for identification of Leishmania species. Samples from 84 Brazilian patients were amplified. Internal transcribed spacer 1 PCR followed by RFLP (HaeIII) [ITS1-RFLP (HaeIII)] identified 46.4% (39/84) of the samples as compatible with the Viannia subgenus. Internal transcribed spacer 1 PCR followed by sequencing (ITS1-sequencing) identified Leishmania (Viannia) braziliensis in 91.7% (77/84) of the TL samples, Leishmania (Leishmania) amazonensis in 3.6% (3/84), L. (V.) guyanensis in 2.4% (2/84), and L. (L.) infantum in 1.2% (1/84). One of the samples showed the same proportion of similarity with L. (V.) guyanensis and L. (V.) panamensis. hsp70 nested PCR followed by RFLP (HaeIII) [nested hsp70-RFLP (HaeIII)] identified 91.7% (77/84) of the samples as compatible with L. (V.) braziliensis/L. (V.) naiffi, 3.6% (3/84) with L. (L.) amazonensis, 1.2% (1/84) with L. (L.) infantum, and 3.6% (3/84) with L. (V.) guyanensis. hsp70 PCR followed by sequencing (hsp70-sequencing) identified L. (V.) braziliensis in 91.7% (77/84) of the TL samples, L. (L.) amazonensis in 3.6% (3/84), L. (V.) guyanensis in 3.6% (3/84), and L. (L.) infantum in 1.2% (1/84). Our findings clearly showed that nested hsp70-RFLP (HaeIII) is better than ITS1-RFLP (HaeIII) and that ITS1 or hsp70 PCR followed by sequencing was adequate for identifying Leishmania species. We also found that Leishmania (Viannia) braziliensis is the most common species causing TL in Brazil. Therefore, sequencing multiple target genes such as ITS1 and hsp 70 is more accurate than RFLP for identifying Leishmania species.

Toxoplasma gondii Infection in the Eurasian Beaver (Castor fiber) in Switzerland: Seroprevalence, Genetic Characterization, and Clinicopathologic Relevance

Toxoplasma gondii is a coccidian parasite able to infect all warm-blooded animals and humans. Rodents are one of the most important intermediate hosts for T. gondii, but little is known about infection in beavers and its clinical relevance. Toxoplasmosis was not considered an important waterborne disease until recently, but with increased outbreaks in humans and animals this perspective has changed. Serum samples from 247 Eurasian beavers (Castor fiber) collected from 2002 to 2022 were tested for antibodies to T. gondii by a commercial ELISA. Antibodies to T. gondii were found in 113 (45.8%) beavers. Higher weight and proximity to urban areas were found to be significant predictors for seropositivity. Additionally, T. gondii DNA was detected in 23/41 brain tissue samples by real-time PCR. Histopathologic examination of brain sections revealed inflammatory changes in 26/40 beavers, mainly characterized by encephalitis, meningitis, choroid plexitis, or a combination of them. In six of these cases the lesions were in direct association with parasitic stages. With an adapted nested PCR multilocus sequence typing and in silico restriction fragment length polymorphism analysis approach, three different T. gondii genotypes were detected in brain samples: the clonal Type II strain (ToxoDB 1), a Type II variant (ToxoDB 3), and a novel genotype exhibiting both Type II and I alleles in a further animal. Toxoplasma gondii infections in beavers have epidemiologic and clinical significance. The high seroprevalence indicates frequent contact with the parasite, and as competent intermediate hosts they may play an important role, contributing to maintaining the life cycle of T. gondii in semiaquatic habitats. In addition, although most beavers appear to develop subclinical to chronic disease courses, acute and fatal outcomes, mainly characterized by encephalitis and generalized infection, do also occur.

Interleukin-8 genetic polymorphism and its relation to Helicobacter pylori infection and Helicobacter pylori-associated gastric diseases

Helicobacter pylori (H. pylori) infection has a variety of clinical outcomes, and host genetic factors play an important role in this process. Cytokines are important factors in mediating and controlling the inflammatory process during H. pylori infection. Interleukin-8 (IL-8) plays a critical role in the epithelial cell response to H. pylori infection and the development of H. pylori-related gastric disorders. The IL-8 gene has an A/T base pair polymorphism in the promoter region (-251), which has been linked to an increase in interleukin production by gastric epithelial cells. In this context, the goal of our study was to determine the polymorphism in the IL-8 gene and its relation to H. pylori infection and H. pylori-associated gastric diseases. Gastric biopsy specimens were collected from 44 patients with H. pylori infection and 29 patients without H. pylori infection. The rapid urease test and detection of the glmM gene were used to diagnose H. pylori infection. Polymerase chain reaction-restriction fragment length polymorphism was used to identify the polymorphism in the Il-8 gene (at position-251). The presence of the A/A and T/A genotypes of the IL-8 gene was found to be significantly associated with susceptibility to H. pylori infection (p = 0.012 and p = 0.004, respectively). Also, the IL-8 A allele was significantly associated with H. pylori infection in our study (p = 0.002). We did not find a significant association between IL-8 gene polymorphism and a higher risk of gastritis and peptic ulcer disease. In conclusion, IL-8 gene polymorphism at -251 position was significantly associated with H. pylori infection.

Molecular confirmation of the systemic toxoplasmosis in cat

INTRODUCTION AND OBJECTIVE

Systemic toxoplasmosis with tissue-spread parasites occurring in intermediate hosts may also occur in immunocompromised cats (e.g., infected with FLV or FIV). To the best of our knowledge, no reports have been published on the detection and genotyping of T. gondii DNA in cats with extraintestinal toxoplasmosis in Poland. The article describes the case of the sudden death of 3 out of 4 cats in a cattery, and the detection and molecular characterization of T. gondii DNA detected in the tissues of one of the dead cats.

MATERIAL AND METHODS

Samples of brain, lungs, heart, and liver of the cat that died suddenly were examined for the presence of T. gondii DNA (B1 gene) by nested PCR and real-time PCR. DNA positive samples were also genotyped at 12 genetic markers using multiplex multilocus nested PCR-RFLP (Mn-PCR-RFLP) and multilocus sequence typing (MLST).

RESULTS

A total of 9 out of the 20 DNA samples were successfully amplified with nested and/or Real-time PCR. DNA from 3 out of 5 types of tested samples were genotyped (brain, heart and muscle). Mn-PCR-RFLP and MLST results revealed type II (and II/III at SAG1) alleles at almost all loci, except a clonal type I allele at the APICO locus. This profile corresponds to the ToxoDB#3 genotype, commonly identified amongst cats in Central Europe.

CONCLUSIONS

To the best of our knowledge, this is the first study describing the genetic characteristics of T. gondii population determined in a cat in Poland. These data confirm the importance of this host as a reservoir for this pathogen, and demonstrate the genotypic variation of this parasite. Veterinarians should take into account that cats may develop disseminated toxoplasmosis, and that it is a systemic disease which may lead to the death of the cat, and to transmission of the pathogen to other domestic animals and to humans.

Phylogenetic Variation of Tri1 Gene and Development of PCR-RFLP Analysis for the Identification of NX Genotypes in Fusarium graminearum Species Complex

NX toxins have been described as a novel group of type A trichothecenes produced by members of the Fusarium graminearum species complex (FGSC). Differences in structure between NX toxins and the common type B trichothecenes arise from functional variation in the trichothecene biosynthetic enzyme Tri1 in the FGSC. The identified highly conserved changes in the Tri1 gene can be used to develop specific PCR-based assays to identify the NX-producing strains. In this study, the sequences of the Tri1 gene from type B trichothecene- and NX-producing strains were analyzed to identify DNA polymorphisms between the two different kinds of trichothecene producers. Four sets of Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods were successfully developed to distinguish the common type B trichothecene producers and NX producers within FGSC. These promising diagnostic methods can be used for high-throughput genotype detection of Fusarium strains as a step forward for crop disease management and mycotoxin control in agriculture. Additionally, it was found that the Tri1 gene phylogeny differs from the species phylogeny, which is consistent with the previous studies.

Application of PCR-RFLP for quick identification of MSTN mutants in MSTN mutant pig breeding

Knockout of the MSTN gene is linked to the enlarged tongue, and it causes suckling difficulty in animals. The suckling difficulty has a severe effect on animal mortality. Thus, special care was required to ensure their survivability. Here, it is critical to promptly ascertain the genotype of all pigs after birth. The main objective of the present study was to develop the restriction enzyme-mediated PCR-RFLP assay for MSTN mutant pig genotyping. To accomplish this, conserved oligonucleotide primer and restriction site were deduced according to the mutated sequence of the MSTN mutant pigs. PCR amplification yielded a 176 bp band for all homozygous MSTN mutant (MSTN-/-), heterozygous MSTN mutant (MSTN+/-) and wild-type (WT) pigs. However, MSTN+/- samples produced two fragments with 176 and 87 bp, and WT samples produced one fragment with 87 bp after being digested by BstNI. MSTN-/- samples were not digested by BstNI and yielded a 176 bp band. Thus, we were able to determine the genotype of all pigs using BstNI restriction enzyme-mediated PCR-RFLP method. Overall, the present study reported a simple and fast PCR-RFLP genotyping method for MSTN mutant pig breeding. The present study may contribute to the establishment of commercial breeding systems and the production of double muscle pigs.

Multiplex PCR-based RFLP assay for early identification of prevalent Mycobacterium leprae genotypes

Mycobacterium leprae is classified into four SNP genotypes and 16 subtypes (from 1A to 4P) that exhibit phylogeographical association reported from around the world. Among them, genotypes 1D and 3I represent more than 60% of M. leprae strains. Here, we report a new method for M. leprae genotyping which identifies the genotypes 1D and 3I by combining multiplex PCR amplification and restriction fragment length polymorphism (RFLP) of a M. leprae DNA amplicons using AgeI restriction enzyme. Agarose gel electrophoresis showed a deletion of 11 bp only among 3I genotypes by electrophoresis. When this multiplex PCR reaction is subjected to AgeI digestion, successful restriction digestion shows three bands for all the genotypes except 1D where only two bands were observed due to loss of restriction site. This method gives us the advantage of 1-step identification of the two most prevalent strains of M. leprae without using specialized equipments such as the Sanger sequencing system or quantitative PCR.

Characterization of mitochondrial 12S rRNA gene of yellow-striped chevrotain (Moschiola kathygre) and white-spotted chevrotain (Moschiola meminna) and development of a PCR-RFLP marker for the unambiguous identification of the species

Tragulids hold a significant place in the evolutionary history of mammals since they represent the basal branch of ruminants. Only three genera of tragulids are being extant to date such as Tragulus, Hyemoschus and Moschiola. In the genus Moschiola, Sri Lankan chevrotains (Moschiola meminna and Moschiola kathygre) are endemic to Sri Lanka while Moschiola indica is present in India. Sri Lankan chevrotains lack information on their population structure, distribution and molecular evidence on species identification. This leads to possible threats including habitat destruction, poaching and illegal hunting and trading under different names. In this study, genomic DNA from hair follicles was isolated from M. meminna and M. kathygre and 12S rRNA mitochondrial gene was amplified using universal primers. The PCR products were sequenced and phylogenetic analysis was done on Sri Lankan chevrotains for the first time. The sequences of Sri Lankan chevrotains share 99.7% similarity as they differ only in a single InDel present in M. meminna. In silico analysis of 12S rRNA region revealed that PCR-RFLP approach can be used to differentiate the Sri Lankan chevrotains from Indian chevrotain using the restriction enzymes; Rsa I, Sca I, Hinf I and Hind III. M. kathygre and M. meminna can be differentiated from each other by using Dra I.

A PCR-Induced Mutagenesis-Restriction Fragment Length Polymorphism Method for the Detection of CRISPR-Induced Indels

As CRISPR-based technologies are widely used for knocking out genes in cell lines and organisms, there is a need for the development of reliable, cost-effective, and fast methods that identify fully mutated clones. In this context, we present a novel strategy named PCR-induced mutagenesis-restriction fragment length polymorphism (PIM-RFLP), which is based on the well-documented robustness and simplicity of the classical PCR-RFLP approach. PIM-RFLP allows the assessment of the editing efficiency in pools of edited cells and the effective identification of fully mutated single-cell clones. It is based on the creation by mutagenic PCR of a restriction enzyme degenerate cleavage site in the PCR product of the wild-type allele, which can then be distinguished from the indel-containing alleles following the standard RFLP procedure. PIM-RFLP is highly accessible, can be executed in a single day, and appears to outperform Sanger sequencing deconvolution algorithms in the detection of fully mutated clones.

Association between MC1R gene and coat color segregation in Shanxia long black pig and Lulai black pig

BACKGROUND

Coat color, as a distinct phenotypic characteristic of pigs, is often subject to preference and selection, such as in the breeding process of new breed. Shanxia long black pig was derived from an intercross between Berkshire boars and Licha black pig sows, and it was bred as a paternal strain with high-quality meat and black coat color. Although the coat color was black in the F1 generation of the intercross, it segregated in the subsequent generations. This study aims to decode the genetic basis of coat color segregation and develop a method to distinct black pigs from the spotted in Shanxia long black pig.

RESULTS

Only a QTL was mapped at the proximal end of chromosome 6, and MC1R gene was picked out as functional candidate gene. A total of 11 polymorphic loci were identified in MC1R gene, and only the c.67_68insCC variant was co-segregating with coat color. This locus isn't recognized by any restriction endonuclease, so it can't be genotyped by PCR-RFLP. The c.370G > A polymorphic locus was also significantly associated with coat color, and has been in tightly linkage disequilibrium with the c.67_68insCC. Furthermore, it is recognized by BspHI. Therefore, a PCR-RFLP method was set up to genotype this locus. Besides the 175 sequenced individuals, another more 1,391 pigs were genotyped with PCR-RFLP, and all of pigs with GG (one band) were black.

CONCLUSION

MC1R gene (c.67_68insCC) is the causative gene (mutation) for the coat color segregation, and the PCR-RFLP of c.370G > A could be used in the breeding program of Shanxia long black pig.

Genotyping methods and their contributions to the study of tuberculosis dynamic in Latin America

INTRODUCTION

Mycobacterium tuberculosis genotyping has impacted evolutionary studies worldwide. Nonetheless, its application and the knowledge generated depend on the genetic marker evaluated and the detection technologies that have evolved over the years. Here we describe the timeline of main genotypic methods related to M. tuberculosis in Latin America and the main findings obtained.

METHODOLOGY

Systematic searches through the PubMed database were performed from 1993 to May 2021. A total of 345 articles met the inclusion criteria and were selected.

RESULTS

Spacer oligonucleotide typing (spoligotyping) was the most widely used method in Latin America, with decreasing use in parallel with increasing use of mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) and whole genome sequencing (WGS). Among the countries, Brazil, Mexico, and Argentina had the most publications, and a considerable part of the articles were in collaboration with Latin American or non-Latin American institutions; a small proportion of studies needed partnerships to perform the genotypic methods. The genotypic methods allowed the identification of M. tuberculosis genotypes with greater capacity for clonal expansion and revealed the predominance of the Euro-American lineage in Latin America. There was a notable presence of the Beijing family in Peru and Colombia.

CONCLUSIONS

The data obtained demonstrated the importance of expanding collaborative networks of tuberculosis (TB) research groups to countries with low productivity in this area, the commitment of the few Latin American countries to advance TB research, as well as the inestimable value of building a Latin America database, considering ease of population mobility between countries.

Association of ABCG2 Polymorphisms on Triple Negative Breast Cancer (TNBC) Susceptibility Risk

OBJECTIVE

The aim of this study was to elucidate the association of ATP-binding cassette super-family G member 2 (ABCG2) gene polymorphisms with individual susceptibility to Triple Negative Breast Cancer (TNBC) as well as clinicopathological variables in TNBC patients. Two common polymorphisms in Asian population, ABCG2 34 G>A and 421 C>A was selected in this study.

METHODS

Blood samples were collected from 75 TNBC patients and 83 controls. Genomic DNA was extracted from blood samples and the SNP genotyping was performed by using PCR-RFLP technique. The genotypes were characterized and grouped into homozygous wildtype, heterozygote and homozygous variant based on the band size. The result was subjected to statistical analysis.

RESULTS

The A allele and AA genotype of ABCG2 421 C>A had OR of 3.011 (p=0.003, 95% CI: 1.417-6.398) and 9.042 (p=0.011, 95% CI: 1.640-49.837), to develop advanced staging carcinoma respectively. The AA genotype of ABCG2 421 C>A polymorphism was also associated with metaplastic and medullary carcinoma with an OR of 6.429 (p=0.018, 95% CI: 1.373-30.109). A significant association was also found in haplotype 34G/421A of ABCG2 with advanced cancer staging as well as metaplastic and medullary carcinoma with OR of 2.347 (p=0.032, 95% CI: 1.010-5.560) and 2.546 (p=0.008, 95% CI: 1.005-6.447), respectively.  Conclusion: The present study suggests that ABCG2 421 C>A polymorphism was associated with metaplastic and medullary histology and advanced cancer staging in TNBC patients.

Advocating for PCR-RFLP as molecular tool within malaria programs in low endemic areas and low resource settings

The road to malaria elimination for low- and middle-income countries is paved with obstacles, including the complexity and high costs of advanced molecular methods for genomic analysis. The usefulness of PCR-RFLP as less complex and affordable molecular surveillance tool in low-endemic malaria regions was assessed in a cross-sectional study conducted in Suriname, currently striving for malaria elimination, but plagued by recent P. vivax outbreaks. Molecular analysis of two highly polymorphic genes Pvmsp-1 F2 and Pvmsp-3α was performed for 49 samples, collected during October 2019 through September 2021 from four different regions with varying malaria transmission risks. RFLP-profiling revealed that outbreak samples from three indigenous villages, almost exclusively, harbored a single clonal type, matching the "Palumeu" lineage previously described in 2019, despite multiple relapses and drug pressure exerted by mass drug administration events, suggesting a limited P. vivax hypnozoite reservoir in Suriname. In contrast, isolates originating from Sophie, a mining area in neighboring French Guiana displayed a highly heterogeneous parasite population consistent with its endemic malaria status, demonstrating the differentiating capacity and thus the usefulness of PCR-RFLP for P. vivax genetic diversity studies. Outbreak reconstruction emphasized the impact of undetected human movement and relapses on reintroduction and resurgence of P. vivax malaria and PCR-RFLP monitoring of circulating parasites guided the roll-out of targeted interventions. PCR-RFLP seems a suitable molecular alternative in low-endemic areas with restricted resources for outbreak analysis, for monitoring the spread or containment of circulating strains and for identification of imported cases or potential foci.

Association of LIN28B Gene Polymorphisms (rs221634, rs221635, rs314276, rs9404590, and rs12194974) with Non-Hodgkin Lymphoma Susceptibility and Clinical/Pathological Features

BACKGROUND AND AIM

Lymphoma is a common hematopoietic cancer.  It has been proposed that LIN28B gene and its variations may have function in cancer progression and metastasis. Therefore, the purpose of this investigation has been to examine the correlation among LIN28B gene polymorphisms (such as rs221634 A>T, rs221635 T> C, rs314276 C>A, rs9404590 T>G, and rs12194974 G>A) as well as the risk of NHL in an Iranian sample.

MATERIALS AND METHODS

In the current case-control research, 175 individuals with Non-Hodgkin Lymphoma along with 175 normal controls participated; polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methodology has been utilized to the genotype samples.

RESULTS

Our data demonstrated that rs12194974 and the rs221635 variants have been correlated with higher NHL risk, while rs221634 and rs314276 variants were correlated with lower risk of NHL (P≤0.05). In addition, we detected an association between rs221634 and treatment with R-CHOP. No substantial correlation has discovered among rs9404590 polymorphism and NHL in any inheritance models (P≥0.05).

CONCLUSION

This was the first investigation evaluating the correlation among LIN28B gene polymorphisms as well as the occurrence of NLH. Further studies in different ethnic populations and large-scale sample size are needed to support results.

Lack of evidence for association between the leptin/Sau3AI gene and milk yield traits in Holstein Friesian dairy cattle

This study aimed to investigate the effect of leptin gene polymorphism and some environmental factors on milk production traits. Blood samples from 212 Holstein Friesian dairy cattle reared on a private farm were used. The intron 2 region of the leptin gene was digested with Sau3AI restriction enzyme using the PCR-RFLP method. A and B alleles and AA, AB, and BB genotype frequencies for the Sau3AI polymorphism were determined as 0.8821 and 0.1179, and 0.764, 0.236 and 0.000, respectively. Chi-square analysis revealed that the leptin gene polymorphism followed the Hardy-Weinberg equilibrium, including the absence of animals with the BB genotype. The effect of leptin gene polymorphism on all milk production traits was insignificant. For milk production traits, direct heritability (ha2) varied between 0.03 ± 0.283 (for the dry period) and 0.50 ± 0.183 (for milk conductivity). Regarding the milking time (MT), the estimated breeding values (EBVs) of cattle with the AA genotype were higher than the AB genotype (P < 0.05). As a result of this study, in the selection program, allele or genotype could not be suggested as a marker for milk yield characteristics except for the possible exception of milking time and its relationship to mastitis incidence.

The Relationship between Complement Components C1R and C5 Gene Polymorphism and the Values of Blood Indices in Suckling Piglets

The main mechanism of innate immunity is the complement system. Its components include the protein products of the C1R and C5 genes, which are involved in the classical activation pathway as well as the inflammatory and cytolytic immune responses, respectively. The aim of this study was to determine the relationship between PCR-restriction fragment length polymorphism in C1R (726T > C) and C5 (1044A > C) genes, and the values of hematological and biochemical blood indices in suckling crossbred (Polish Large White × Polish Landrace × Duroc × Pietrain) piglets (n = 473), considering their age (younger, 21 ± 3 days, n = 274; older, 35 ± 3 days, n = 199) and health status. The frequencies of the C5 genotypes deviated from the Hardy-Weinberg expectations. Younger piglets, healthy piglets, piglets that deviated from physiological norms and older piglets with the C1R TT genotype all had lower white and red blood cell indices. In piglets with the C5 CC genotype, younger piglets, piglets that deviated from physiological norms and older piglets, a greater number and/or percentage of monocytes were recorded in the blood. Older piglets also showed an increase in the number of leukocytes and granulocytes, along with a tendency for a decrease in the percentage of lymphocytes in their blood. We concluded that a polymorphism in the C1R gene may exhibit a functional association or genetic linkage with other genes involved in the process of erythropoiesis. Furthermore the relationship between the C5 gene polymorphism and the number and/or percentage of monocytes in the blood may modify the body's defense abilities. Piglets with the CC genotype, having an increased number/proportion of these cells in their blood, probably display a weakened immune response to pathogens or a chronic stimulation of the immune system.

A new variant of the ectodysplasin A receptor death domain gene associated with anhidrotic ectodermal dysplasia in a Turkish family and its simple diagnosis by restriction fragment length polymorphism

Ectodermal dysplasia (ED), which exhibits a wide range of clinical symptoms, may be classified into three major types: hypohidrotic, anhidrotic, and hidrotic. A male child (proband) showing anhidrotic dysplasia was used as the subject of this study. The biopsy of the big toe revealed that the male child had no sweat glands. Genetic analysis of the patient revealed a mutation caused by a homozygous nucleotide substitution in the EDAR-associated death domain (EDARADD) (rs114632254) gene c.439G>A (p.Gly147Arg). Phenotypically, his teeth were sharp, but eight teeth were missing (oligodontia). The patient had normal nails with dry skin, sparse hair, everted lower lip vermilion, hyperpigmented eyelids, and abnormal nasal bridge morphology around the eyes. There is also a homozygous dominant (healthy) female and a heterozygous male in this family, who are cousins (aunt children) to the heterozygous parents. The daughter of the patient was also heterozygous. This mutation represents homozygous recessive inheritance, which we describe for the first time. Furthermore, we demonstrated that this genetic disorder can be readily diagnosed using the restriction fragment length polymorphism (RFLP) method after digestion with MnII restriction endonuclease.

Novel association between single-nucleotide polymorphisms of IKKβ at rs17875746 and rs12676482 and periodontitis

BACKGROUND

Single-nucleotide polymorphisms (SNPs) in the IKKβ gene have been associated with susceptibility to various inflammatory illnesses, including periodontitis.

OBJECTIVES

The aim of the present study was to investigate the association between IKKβ SNPs (at rs17875746 and rs12676482) and periodontitis in an Iraqi Arab population.

MATERIAL AND METHODS

In this case-control study, 94 Iraqi volunteers were split into 2 groups, with the case group including 62 periodontitis patients (37 men and 25 women) and the control group including 32 racially matched healthy people (19 men and 13 women). Periodontal parameters were recorded for each individual. Then, 2 mL of venous blood was taken from each participant to isolate their genomic DNA. In particular, the genotyping of rs17875746 and rs12676482 in IKKβ was performed with the use of the polymerase chain reaction (PCR) sequencing methods.

RESULTS

The effect of the distribution of IKKβ SNPs on periodontitis was assessed by counting the odds ratio (OR), which was 5.264 for rs17875746 and 0.900 for rs12676482. Surprisingly, allele T revealed a significantly higher association with periodontitis for rs17875746 (OR = 6.750) than allele G (p = 0.038). Overall, the GT genotype in rs17875746 had a higher chance of developing the disease (OR = 3.321) as compared to other genotypes. Meanwhile, the GA genotype in rs12676482 had a higher chance of developing the disease (OR = 1.242) as compared to other genotypes. In addition, rs17875746 showed a significant positive association with tooth mobility, a family history, clinical attachment loss (CAL), and gingival recession (GR) in the study groups.

CONCLUSIONS

The IKKβ polymorphisms may increase genetic susceptibility to periodontitis in Iraqi Arab patients.

Genotyping of toxoplasma gondii isolates from México reveals non-archetypal and potentially virulent strains for mice

Genotyping and virulence studies of Toxoplasma gondii are essential to investigate the pathogenesis of strains circulating worldwide. In this study, eight T. gondii isolates obtained from a congenitally infected newborn, a calf, two cats, three dogs, and a wallaby from five states of México were genotyped by Mn-PCR-RFLP with 11 typing markers (SAG1, SAG2 5'3', alt. SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico), five virulence markers (CS3, ROP16, ROP17, ROP18 and ROP5), 15 microsatellite markers (TUB-2, W35, TgM-A, B18, B17, M33, IV.1, XI.1, M48, M102, N60, N82, AA, N61, N83), and sequencing. A phylogenetic network was built to determine the relationship between Mexican isolates and those reported worldwide. Six different genotypes were identified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), ToxoDB #8, #10, #28 (n = 3), #48, #116, and #282. Genotyping by microsatellite analysis differentiated the three PCR-RFLP genotype #28 isolates into two strains, revealing a total of seven microsatellite genotypes. Three different allele combinations of ROP18/ROP5 virulence markers were also found, 3/3, 1/1, and 4/1. The last two combinations are predicted to be highly virulent in the murine model. According to the phylogenetic network, the T. gondii strains studied here are related to archetypal strains I and III, but none are related to the strains previously reported in México. The genotypes identified in this study in different species of animals demonstrate the great genetic diversity of T. gondii in México. The ToxoDB-PCR-RFLP #28 genotype was found in three isolates from different hosts and states. Additionally, four of the isolates are predicted to be highly virulent in mice. The next step will be to perform in vitro and in vivo assays to determine the phenotype of these T. gondii isolates in murine models.

The C/A functional polymorphism of TGF-β2 gene (rs991967) in primary open angle glaucoma patients

BACKGROUND

Primary Open-angle Glaucoma (POAG) is a functional disease that.leads to blindness globally. The aims of this study are estimation the importance.of transforming growth factor-beta 2 (TGF-β2) in the pathogenicity of POAG and.to evaluate the effect of the C/A SNP of the TGF-β2 gene (rs991967) on POAG development.

METHODS

Blood samples and some topographic data were collected from POAG.patients and the controls. The serum level of TGF-β2 was estimated by ELISA.and the C/A SNP of the TGF-β2 gene (rs991967) was determined by RFLP-PCR.

RESULTS

The males are more susceptible to having POAG (p = 0.0201). The serum.TGF-β2 is higher in POAG patients as compared with the control (p < 0.0001). The.AA (reference) genotype was the most common in the patients (61.7%). While..CC genotype (45.0%, OR: 0.136, 95%CI: 0.05-0.36, P < 0.0001) and AC..genotypes (41.7%, OR: 0.051, 95%CI: 0.01-0.16, P < 0.001) were most common..in the control group. Moreover, the TGF-β2 C allele is protective (OR: 0.25,..95%, CI: 0.15-0.44, P < 0.0001). Patients with AA, CC, and AC genotypes have..significantly high levels of TGF-β2 (P < 0.001) than the control.

CONCLUSIONS

The males were more susceptible to acquiring POAG than females,.. especially the elderly. The TGF-β2 plays important role in the pathogenesis of POAG. The CC and AC genotypes are common in the control and the C allele is a protective factor.

Molecular and morphological studies on Contracaecum rudolphii A and C. rudolphii B in great cormorants (Phalacrocorax carbo sinensis) from Italy and Israel

The distribution of parasites is shaped by a variety of factors, among which are the migratory movements of their hosts. Israel has a unique position to migratory routes of several bird species leaving Europe to winter in Africa, however, detailed studies on the parasite fauna of birds from this area are scarce. Our study investigates occurrence and distribution of sibling species among Contracaecum rudolphii complex in Phalacrocorax carbo sinensis from Italy and Israel, to acquire further information on the geographical range of these species to gain deeper knowledge on the ecology of these parasites and their bird host. A total of 2383 Contracaecum were collected from the gastric mucosa of 28 great cormorants (18 from Israel and 10 from Italy). A subsample was processed for morphological analyses in light and scanning electron microscopy (SEM), and for molecular analyses through amplification and sequencing of the ITS rDNA and the cox2 mtDNA, and through PCR-RFLP. All the 683 Contracaecum subjected to molecular identification belonged to C. rudolphii s.l., (300 C. rudolphii A and 383 C. rudolphii B). SEM micrographs provided, for the first time, details of taxonomic structures in male specimens from both sibling species, and the first SEM characterization of C. rudolphii B. This work presents the first data on the occurrence of sibling species of C. rudolphii in Israel and provides additional information on the distribution of C. rudolphii A and B in Italy, confirming the high prevalence and intensity of infection observed in Ph. carbo sinensis from other Italian areas.

Molecular detection of Toxoplasma gondii, Neospora caninum and Sarcocystis spp in tissues of Sus scrofa slaughtered in southern Brazil

The aim of this study was to determine the presence of deoxyribonucleic acid (DNA) from Toxoplasma gondii, Sarcocystis spp. and Neospora caninum, in tissues of wild boars slaughtered in southern Brazil. A total of 156 samples were collected from different organs of 25 wild boars, and DNA from at least one of the protozoa investigated was detected in 79 samples. To differentiate between infectious agents, restriction fragment length polymorphism was performed using the restriction enzymes DdeI and HpaII. For N. caninum, conventional PCR was performed with specific primers. The DNA of at least one of the studied pathogens was detected in each animal: 26.58% for T. gondii, 68.36% for Sarcocystis spp. and 5.06% for N. caninum. Coinfection between T. gondii and Sarcocystis spp. occurred in 14 animals, between T. gondii and N. caninum in only one male animal, between Sarcocystis spp. and N. caninum in a female, while co-infection with the three agents was equally observed in only one male animal. Considering the high frequency of detection and its zoonotic risk, especially T. gondii, it appears that wild boars can be potential sources of transmission of infectious agents and the adoption of monitoring measures in these populations should be prioritized.

Identification of Burkholderia mallei Isolates with Polymerase Chain Reaction-Restriction Fragment Length Polymorphism

Burkholderia mallei is the main cause of glanders as a dangerous contagious zoonosis disease that is mostly observed in single-hoofed animals, especially horses. Modern molecular techniques have been recently employed to improve epidemiology for identifying and searching for strains of this bacterium at different times and locations. Due to the unknown number of circulating strains and lack of preventive methods, glanders is still observed in the form of epidemics. The present study aimed to evaluate six field isolates plus two laboratory strains of Borkolderia mallei and Burkholderia pseudomallei using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. All the isolates and strains were microbially cultured in the glycerol nutrient and glycerol agar media. The individually grown colonies of the bacterium were used in the biochemical tests. The DNA of isolates was extracted by boiling, and the PCR-RFLP test was conducted on their genome. Finally, the bacterium was injected into guinea pigs to induce the Straus reaction. The biochemical assays (or bioassays) confirmed the isolates as Burkholderia mallei. The PCR-RFLP assay demonstrated a product for Burkholderia mallei with a length of 650 bp. Nevertheless, 250 and 400 bp were produced for Burkholderia pseudomallei. The swollen scrotum pointed to the occurrence of the Straus reaction. The PCR-RFLP is a proper differential diagnosis technique for B. mallei; moreover, it is a suitable method for differentiating between Burkholderia mallei and Burkholderia pseudomallei. This technique can detect Burkholderia mallei in a short time with high precision and sensitivity.

A Novel 16S rRNA PCR-Restriction Fragment Length Polymorphism Assay to Accurately Distinguish Zoonotic Capnocytophaga canimorsus and C. cynodegmi

The zoonotic bacteria Capnocytophaga canimorsus and C. cynodegmi, the predominant Capnocytophaga species in the canine oral biota, can cause human local wound infections or lethal sepsis, usually transmitted through dog bites. Molecular surveying of these Capnocytophaga species using conventional 16S rRNA-based PCR is not always accurate due to their high genetic homogeneity. In this study, we isolated Capnocytophaga spp. from the canine oral cavity and identified them using 16S rRNA and phylogenetic analysis. A novel 16S rRNA PCR-restriction fragment length polymorphism (RFLP) method was designed based on our isolates and validated using published C. canimorsus and C. cynodegmi 16S rRNA sequences. The results showed that 51% of dogs carried Capnocytophaga spp. Among these, C. cynodegmi (47/98, 48%) was the predominant isolated species along with one strain of C. canimorsus (1/98, 1%). Alignment analysis of 16S rRNA sequences revealed specific site nucleotide diversity in 23% (11/47) of the C. cynodegmi isolates, which were misidentified as C. canimorsus using previously reported species-specific PCR. Four RFLP types could be classified from all the isolated Capnocytophaga strains. The proposed method demonstrates superior resolution in distinguishing C. cynodegmi (with site-specific polymorphism) from C. canimorsus and especially in distinguishing C. canimorsus from other Capnocytophaga species. After in silico validation, this method was revealed to have an overall detection accuracy of 84%; notably, accuracy reached 100% in C. canimorsus strains isolated from human patients. Overall, the proposed method is a useful molecular tool for the epidemiological study of Capnocytophaga in small animals and for the rapid diagnosis of human C. canimorsus infections. IMPORTANCE With the increased number of small animal breeding populations, zoonotic infections associated with small animals need to be taken more seriously. Capnocytophaga canimorsus and C. cynodegmi are part of common biota in the mouths of small animals and can cause human infections through bites or scratches. In this study, C. cynodegmi with site-specific 16S rRNA sequence polymorphisms was erroneously identified as C. canimorsus during the investigation of canine Capnocytophaga by conventional PCR. Consequently, the prevalence of C. canimorsus is incorrectly overestimated in epidemiological studies in small animals. We designed a new 16S rRNA PCR-RFLP method to accurately distinguish zoonotic C. canimorsus from C. cynodegmi. After validation against published Capnocytophaga strains, this novel molecular method had high accuracy and could detect 100% of C. canimorsus-strain infections in humans. This novel method can be used for epidemiological studies and the diagnosis of human Capnocytophaga infection following exposure to small animals.

PCR-RFLP Analysis of Insulin-Like Growth Factor 2 Gene Polymorphisms in Two Commercial Broiler Chicken Strains (Cobb 500 and Hubbard F-15) and Their Associations with Performance Traits

The present research aimed to study the polymorphisms of the chicken insulin-like growth factor 2 (IGF2) in two commercial broiler breeds (Cobb 500 and Hubbard F-15). In total, 300 avian blood samples were obtained. The genomic DNA was isolated using a fast salt-extraction technique. Moreover, polymerase chain reaction (PCR) was used to amplify 1146 bp fragments of the gene. The amplified fragments were subjected to restriction enzyme digestion using the HinfI endonuclease enzyme, and the digested products were separated on a 2% agarose gel. The findings indicated that there were two alleles T and C for the target locus, with frequencies of 73.3% and 26.7%, respectively. Three distinct genotype variations, TT, TC, and CC, were found, with genotype frequencies of 59.1%, 28.4%, and 12.5%, respectively. A test based on actual and anticipated frequencies of various genotypic variances of the IGF2 gene revealed that the divergence from Hardy-Weinberg equilibrium was not significant (P≤0.01) in commercial broiler breeds (Cobb 500 and Hubbard F-15) chickens. In addition, it was found that birds with genotype TC had a greater body mass at 8 weeks of age, compared to those with genotypes TT and CC. It was determined that the IGF2 gene exhibited a significant degree of variability and might be regarded as a possible genetic marker in selection and breeding programs for poultry.

Genetic polymorphism of RAD51 influences susceptibility to colorectal cancer in Chinese population

OBJECTIVE

The present study aimed to explore whether RAD51 polymorphism confers risk to colorectal cancer.

PATIENTS AND METHODS

A total of 240 patients with colorectal cancer were selected. 390 healthy people who participated in normal physical examinations during the same period were selected as the control group. The polymorphism of RAD51 gene was detected by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. An updated meta-analysis was also conducted.

RESULTS

Meta-analysis found no significant association between the RAD51 polymorphism and CRC risk (all p>0.05). PCR-RFLP method detected three kinds of genotypes (GG, GC, and CC) in both the colorectal cancer group and the control group. A significant association was only found in GC genotype (p<0.05).

CONCLUSIONS

Our results demonstrated that RAD51 polymorphism has a crucial role in colorectal cancer risk and that GC genotype confers an increased risk of colorectal cancer in the Chinese population. The updated meta-analysis indicates that RAD51 polymorphism contributes no risk to colorectal cancer.

MCP-1-2518 (A>G) polymorphism and asthma risk: a pilot case-control study in Cameroon

Introduction

there is little data on the genetic determinants of asthma in Cameroon and sub-Saharan Africa, yet the involvement of genetics in the pathogenesis of this disease has been reported in the literature for several years. This study aims to investigate the possible role of MCP-1 2518 for the risk of asthma in Cameroonians.

Methods

we performed a case-control study on 30 volunteers suffering from asthma, matched by aged and sex to 30 healthy subjects. We determine the polymorphism of MCP-1 2518 using restriction fragment length polymorphism following Polymerase Chain Reaction (RFLP-PCR). Fisher exact test was used to compare proportions, with a threshold of significance set at 0.05.

Results

the average age of cases was 21±10 years with 17 (56.7%) females. The distribution of the MCP-1-2518 (A>G) gene polymorphism in people with asthma was as follows: 3 for AA, 5 for GG, and 22 for AG. The minor G allele was predominant (90%) in people with asthma. It was significantly associated with asthma whether the genotype was heterozygous AG or homozygous GG (p<0.01).

Conclusion

MCP-1-2518 (A>G) shows an association with asthma in our sample. Future larger studies evaluating several polymorphisms are needed to describe the genetic determinants of asthma in Cameroon and sub-Saharan Africa.

Genetic polymorphism of fatty acid binding protein-2 in hyperlipidemic Asian Indians in North India

BACKGROUND

Fatty acid binding protein-2 (FABP-2) is involved in the metabolism of lipids in the intestine. FABP-2 Ala54Thr polymorphism involves a transition of G to A at codon 54 of FABP-2, resulting in an amino acid substitution Ala54 to Thr54 and is associated with elevated fasting triglycerides in some hyperlipidemic populations. In current genome builds and gene databases the variant of the Ala54Thr FABP-2 (rs 1 799 883) is annotated as c.163A>G (p. Thr55Ala).

AIM AND OBJECTIVE

The status of this polymorphism in hyperlipidemic Asian Indians from North India has not been investigated. This study was aimed to evaluate the distribution of the polymorphic variants of the Ala54Thr FABP-2 and their association with lipids in hyperlipidemic subjects.

METHODS

Ala54Thr FABP-2 polymorphism in both hyperlipidemic (n = 210) and normolipidemic (n = 342) subjects was assessed by PCR-RFLP.

RESULTS

Ala54Thr genotypes and alleles distribution did not differ between the hyperlipidemic and normolipidemic groups. The heterozygous genotype FABP-2 Ala/Thr was significantly associated with higher levels of triglycerides and very low-density lipoproteins as compared to the homozygous variant (Thr/Thr) genotype and the wild type homozygous (Ala/Ala) genotype.

CONCLUSIONS

The heterozygous genotype FABP-2 Ala54Thr is a risk factor for the development of hypertriglyceridemia and increased levels of VLDL-c in Asian Indians from North India.

Molecular prevalence and genetic diversity of Toxoplasma gondii in free range chicken in Northeastern Libya

Background: Toxoplasma gondii is one of the zoonotic protozoa parasites. It can prevalently infect humans and warm-blooded animals, causing human health problems and substantial economic losses to the livestock industry worldwide. Chicken is one of the potential sources of toxoplasmosis, but there is no report of the prevalence of toxoplasmosis and their genotypes in free-range chickens in Libya. Aim: The current study aims to conduct a survey of molecular prevalence and identify the Toxoplasma gondii genotype in free-range chickens and its association with the risk factors of age, gender, and region in Northeastern Libya. Methods: This study was conducted by examining a total of 315 free-range chicken organs (brain and heart) derived from three administrative districts in Northeastern Libya. The molecular prevalence was determined by PCR technique using B1 gene amplification and the Toxoplasma gondii genotype was determined by nested PCR-RFLP of GRA6 gene amplicon with restriction enzymes (MseI). Results: The overall molecular prevalence of Toxoplasma gondii in free-range chicken in all three districts was 9.5% (30/315), and the highest (15.4%) was in the Al-Marj district (p =0.01; ?2 =9.238). The highest prevalence of Toxoplasma gondii by age was in chickens aged more than two years (p = 0.001; ?2 = 15.530). The difference in Toxoplasma gondii prevalence in male and female chickens was not significant (p = 0.372; ?2 = 0.798). The predominant genotype I (93.3%) had identified at position 544 bp and 194 bp at the GRA6 marker, and only two positives were from genotype II (6.7%) at 700 bp and 100 bp fragment. Conclusion: The molecular prevalence of toxoplasmosis in free-range chicken in three districts in Northeastern Libya was 9.5%, and the highest rate was shown in the Al Marj district. Chicken by age more than two years had more risk to transmit toxoplasmosis in human. There was no different infection risk by consuming male or female free-range chicken. It is the first report to determine the predominant genotype, which was genotype I.

FAM111B dysregulation promotes malignancy in fibrosarcoma and POIKTMP and a low-cost method for its mutation screening

INTRODUCTION

Mutations in the uncharacterised human FAM111B gene are associated with POIKTMP, a rare multi-organ fibrosing disease. Recent studies also reported the overexpression of FAM111B in specific cancers. Moreover, FAM111B mutation screening may prove expensive in under-resourced facilities. Therefore, this study investigated its cellular function and dysfunction and described an inexpensive mutation screening method.

MATERIALS AND METHODS

FAM111B expression was assessed in silico and validated in vitro in cell lines and primary skin fibroblasts from a South African POIKTMP-patient with the heterozygous FAM111B gene mutation: NM_198947.4: c.1861T>G (p. Tyr621Asp or Y621D) by qPCR and western blot. The cellular function of FAM111B was studied in HT1080 using various cell-based functional assays, and the Y621D mutation was genotyped by PCR-RFLP.

RESULTS

Expression studies showed upregulated FAM111B mRNA and protein in the cancer cells. High FAM111B expression with robust nuclear localization occurred in HT1080. Additionally, expression data and cell-based assays indicated that FAM111B led to the upregulation of cell migration, decreased cell apoptosis, and modulatory effects on cell proliferation. Y621D mutation showed similar effects on cell migration but minimal impact on cell apoptosis. FAM111B mRNA and protein expression were markedly downregulated (p ≤ 0.05) in the POIKTMP-patient's fibroblasts. The PCR-RFLP method successfully genotyped Y621D gene mutation.

DISCUSSION

FAM111B is a cancer-associated nuclear protein: Its modulation by mutations or overexpression may contribute to the malignancy of cancers and POIKTMP/fibrosis and poor clinical outcomes and represents a viable prognostic marker or therapeutic target. Furthermore, the PCR-RFLP method could prove a valuable tool for FAM111B mutation validation or screening in resource-constrained laboratories.

XRCC3 and NBS1 gene polymorphisms modulate the risk of pre-oral cancer and oral cancer in the North Indian population

BACKGROUND

Oral cancer is alarming disease in the developing countries like India. DNA repair capacity may affect by genetic polymorphisms in DNA repair genes and thus may cause to cancer. XRCC3 involves in homologous recombination repair pathway and repair DNA damage and crosslinks while, NBS1 participate in repair of double strand DNA break and starts the cell-cycle checkpoint signaling.

AIMS AND OBJECTIVES

This study was to conducted to find the association of XRCC3, NBS1 polymorphisms with oral disease.

RESULTS

TT genotype of XRCC3 was associated with high risk of precancerous lesions and oral cancerous lesions (P value=0.0001, OR=9.68, 95% CI=2.82-33.21; and P value=0.0001, OR=13.10, 95% CI=3.38-50.73 respectively). We did not observe any interactions of XRCC3 polymorphism with demographic parameters in influencing the risk of oral diseases. Variant allele genotypes (CG, GG) of NBS1 (C>G) polymorphism showed protective association with Oral submucous fibrosis (OSMF), lichen planus as well as oral cancer (OR=0.31, OR=0.01; OR=0.39, OR=0.03; OR=0.43, OR=0.31 respectively). Particularly, tobacco chewer with CG & GG genotypes were at decrease risk of oral diseases (P value=0.02, OR=0.32, 95% CI=0.12-0.80). Compared to CC/CC combined genotype CG/CC, CG/CT, GG/CC and CG/CT genotypes decreased the risk of oral disease (OR=0.05, 0.47, 0.26 & 0.14 respectively).

CONCLUSION

This study concludes that SNP in XRCC3, NBS1 affects susceptibility to oral disease.

A Molecular Diagnostic Assay for the Discrimination of Aphid Species (Hemiptera: Aphididae) Infesting Citrus

Aphid species (Hemiptera: Aphididae) are among the most serious pests for citrus cultivation throughout the world causing substantial crop damages. Accurate identification of aphids to the species level can be difficult, though being crucial for their effective management. In this study, a molecular diagnostic assay for distinguishing eleven aphid species was developed. A fragment of the mitochondrial Cytochrome Oxidase I (mtCOI) gene was used and a Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-FLP) analysis with five restriction enzymes, based on DNA sequence polymorphisms, was applied to differentiate the eleven aphid species. This molecular technique allows aphid species at any life stage to be discriminated accurately and simply and can be a useful tool for monitoring the populations of economically important aphid species.

Comparative Analysis of Molecular RFLP and SNP Markers in Assessing and Understanding the Genetic Diversity of Various Chicken Breeds

Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry.

Isolation and characterization of Toxoplasma gondii isolates from human congenital toxoplasmosis cases reveal a new virulent genotype in São Paulo, Brazil

Toxoplasma gondii causes severe disease in congenitally infected fetuses. The severity of fetal infection is related to the gestational stage at the time of maternal infection, parasite burden, and genotypic characteristics. South America has a high incidence of congenital toxoplasmosis and has the highest genotypic diversity of the parasite. In Brazil, clinical toxoplasmosis in children is notorious, however there are very limited data regarding the strains recovered from congenital infections. In this study, T. gondii strains from two cases of severe congenital toxoplasmosis from the São Paulo metropolitan area were isolated (TgHumIMTBr2 and TgHumIMTBr3) and biologically and molecularly characterized using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and microsatellite analysis, revealing a new non-archetypal virulent genotype designated as #318. The other isolate, genotype #175, has already been described in domestic and wild animals in Brazil, but is now associated with acute toxoplasmosis in humans. These data reinforce the role of non-archetypal T. gondii genotypes in the severity of human congenital toxoplasmosis, highlighting the importance of studies focused on parasite isolation and genotyping for a better understanding of the virulence of isolates from human toxoplasmosis and contributing to the knowledge of the diversity of T. gondii in Brazil.

Early Detection and Identification of Parasitoid Wasps Trichogramma Westwood (Hymenoptera: Trichogrammatidae) in Their Host Eggs Using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism

Parasitoid wasps are invaluable agents in pest biological control. Early detection and identification of parasitoid immatures are vital in characterizing parasitoid-host interactions and for evaluating parasitism rates accurately in the field. Trichogramma is the most widely used parasitoid wasp, and several studies have been performed for its molecular identification. However, those studies were mainly focused on Trichogramma adults and rarely on immatures. Here, we report a method to detect and identify Trichogramma larvae in their host eggs. We designed a pair of Trichogramma-specific primers that amplified Trichogramma mtCOI sequences from Corcyra cephalonica (Stainton) eggs parasitized by any of eight Trichogramma species tested but not from nonparasitized eggs of four lepidopteran hosts. This PCR method reliably detected Trichogramma immatures in parasitized eggs as early as 1 h after parasitism. We further developed an RFLP (restriction fragment length polymorphism) assay using restriction enzymes SspI and VspI to differentiate eight Trichogramma species at their immature stage. Overall, we developed a sensitive and reliable PCR-RFLP method to detect and identify immature-stage Trichogramma in their lepidopteran hosts. This method shows promise for conveniently identifying Trichogramma in insectaries and accurately evaluating parasitism rates in the field.

Molecular detection of fluoroquinolone-resistant Neisseria meningitidis by using mismatched PCR-restriction fragment length polymorphism technique

Ciprofloxacin (CIP) is a commonly used antibiotic for meningococcal chemoprophylaxis, and the mutations in the quinolone resistance-determining region of gyrA are associated with CIP-resistant Neisseria meningitidis. Here, we established a mismatched PCR-restriction fragment length polymorphism (RFLP) assay to detect a mutation at codon 91 of gyrA, followed by high-level CIP-resistant meningococci. We designed PCR-RFLP primers to detect the T91I mutation in gyrA by introducing an artificial AciI cleavage site. This assay was performed using 26 N. meningitidis strains whose gyrA sequences have been characterized. The amplified 160 bp PCR product from gyrA was digested into three fragments (80, 66, and 14 bp) when there was no mutation, or two fragments (146 and 14 bp) when there was a mutation at codon 91. A correlation was observed between the mismatched PCR-RFLP assay and gyrA sequencing. This rapid, simple, and accurate assay has the potential to detect CIP-resistant N. meningitidis in clinical microbiology laboratories, contributing to the appropriate antibiotic selection for meningococcal chemoprophylaxis, will help maintain an effective treatment for close contacts of IMD patients, and prevent the spread of CIP-resistant N. meningitidis.

Cas12a-Based Diagnostics for Potato Purple Top Disease Complex Associated with Infection by 'Candidatus Phytoplasma trifolii'-Related Strains

'Candidatus Phytoplasma trifolii' is a cell wall-less phytopathogenic bacterium that infects many agriculturally important plant species such as alfalfa, clover, eggplant, pepper, potato, and tomato. The phytoplasma is responsible for repeated outbreaks of potato purple top (PPT) and potato witches' broom (PWB) that occurred along the Pacific Coast of the United States since 2002, inflicting significant economic losses. To effectively manage these phytoplasmal diseases, it is important to develop diagnostic tools for specific, sensitive, and rapid detection of the pathogens. Here we report the development of a DNA endonuclease targeted CRISPR trans reporter (DETECTR) assay that couples isothermal amplification and Cas12a transcleavage of fluorescent oligonucleotide reporter for highly sensitive and specific detection of 'Candidatus Phytoplasma trifolii'-related strains responsible for PPT and PWB. The DETECTR assay was capable of specifically detecting the 16S-23S ribosomal DNA intergenic transcribed spacer sequences from PPT- and PWB-diseased samples at the attomolar sensitivity level. Furthermore, the DETECTR strategy allows flexibility to capture assay outputs with fluorescent microplate readers or lateral flow assays for potentially high-throughput and/or field-deployable disease diagnostics.

Effects of UGT2B7 rs7662029 and rs7439366 polymorphisms on sublingual buprenorphine metabolism in heroin addicts: An improved PCR-RFLP assay for the detection of rs7662029 polymorphism

This study aimed to determine the effects of UGT2B7 rs7662029 and rs7439366 polymorphisms on plasma buprenorphine (BUP) concentration and different treatment responses in a sample of 109 patients with opioid use disorder (OUD) treated with sublingual BUP/naloxone. Polymorphisms were analysed by PCR-RFLP. Plasma concentrations of BUP and its metabolite norbuprenorphine were detected by LC-MS/MS. Craving, withdrawal, depression and anxiety were measured by appropriate scales. OUD patients with rs7439366 CC or rs7662029 GG genotypes had significantly lower dose-normalized (BUP/D) and dose/kg-normalized BUP (BUP/D.kg^-1) levels than those who were CT or AA carriers. Significant associations between UGT2B7 rs7662029 and increased craving (p = 0.037) and withdrawal symptoms (p = 0.029) were detected. Our findings were pointing to an important role of UGT2B7 in the metabolism of sublingual BUP/naloxone in the heroin addicts for the first time. A novel PCR-RFLP assay was developed for the determination of UGT2B7 rs7662029 polymorphism, based on utilizing novel restriction enzyme.