Development of a gp60-subtyping method for Cryptosporidium felis

BACKGROUND

Feline cryptosporidiosis is an increasing problem, especially in catteries. In humans, close contact with cats could be a potential source of infection although the risk of contracting cryptosporidiosis caused by Cryptosporidium felis is considered to be relatively low. Sequencing of the 60-kDa glycoprotein gene is a commonly used tool for investigation of the genetic diversity and transmission dynamics of Cryptosporidium species. However, until now the sequence of gp60 from C. felis has not been available and genotyping has been limited to less discriminatory markers, such as 18S rRNA, COWP and HSP70.

METHODS

We have identified the gp60 orthologue within the genome sequence of C. felis, and used the sequence to design a nested PCR for subtyping purposes. A total of 128 clinical isolates of both feline and human origin, were used to evaluate the marker.

RESULTS

Sequence analysis revealed large variations between the different samples. The C. felis gp60 lack the characteristic serine-tract found in many other cryptosporidian orthologues, instead it has an insertion of variable length (361-742 nt). Also, two cases of suspected zoonotic transmission of C. felis between cats and humans were successfully confirmed.

CONCLUSIONS

We have identified the gp60 gene in C. felis and show how this highly variable marker can be used in epidemiological investigations.

The Association between ABCB1 C1236T/C3435T SNPs and H. pylori Infection among Jordanians

Infection with Helicobacter pylori (H. pylori) is very common and affecting about 50% of the worldwide population. Several genetic variations have been implicated in determining the clinical susceptibility to this infection. In the current study, we examined the association between C1236T (rs1045642) and C3435T (rs1045642) single nucleotide polymorphisms (SNPs) in the ABCB1 gene and the prevalence of H. pylori infection among Jordanians. A total of 412 subjects (257 H. pylori-positive cases and 155 H. pylori-negative controls) were recruited and participated in the study, and the genotyping of the ABCB1 gene was performed using RFLP-PCR techniques. A significant association was detected between C1236T and H. pylori infection (p < 0.01). The frequency of CT genotype was significantly higher in the positive cases (40.1%) compared to the controls (21.3%). In addition, the C3435T SNP was weakly associated with H. pylori infection (p = 0.077). Haplotype analysis of C1236T and C3435T SNPs showed that the TT haplotype was present in 22.7% of the positive cases compared to 30.7% of the negative controls (p < 0.05, odds ratio = 0.663, 95% CI: (0.483-0.911)). Consequently, the TT haplotype seems to decrease the risk of H. pylori infection. In conclusion, the current results suggest an association between ABCB1 SNPs and H. pylori infection in the Jordanian population.

Isolation and Genotyping of Toxoplasma gondii Strains

Toxoplasma gondii is a protozoan parasite that infects mammals and birds. Molecular epidemiology and population genetic studies have revealed widespread and distinct distribution of different T. gondii genotypes globally. Animals (domestic and wild) are the reservoirs for transmission of this parasite to humans. Recent development in molecular genotyping methods allowed us to identify parasite strains with high resolution and to dissect transmission patterns among different hosts. However, current data in the literature is still limited and fragmented. Here, we summarize a set of protocols that can be used to identify T. gondii infection in clinically normal animals, isolate the parasite by bioassay using animal tissues, extract parasite DNA from tissue samples, and finally identify the parasite by multilocus PCR-RFLP genotyping. We hope these protocols provide essential tools to study genetic diversity, population structure and transmission dynamics of T. gondii. Accumulation of the information will allow us to better understand, control, and prevent T. gondii infection in the future.

Polymorphism of Glutathione S-transferase Genes and the Risk of Toxic Liver Damage in Petrochemical Workers

BACKGROUND

Exposure to numerous chemicals, including industrial ones, may result in liver damage. The body susceptibility to the environmental hazards largely depends on the activity of the enzymes in the xenobiotic detoxification system. Function abnormalities of such enzymes due to genetic variations would increase the risk of developing various diseases.

OBJECTIVE

To elucidate the relationship between polymorphism in glutathione S-transferase genes (GSTM1, GSTT1 and GSTP1) and the risk of toxic liver damage in a group of petrochemical workers.

METHODS

This study was conducted on 72 workers with toxic liver injury, 156 healthy workers, and 322 healthy individuals without history of occupational exposure to chemicals. Genotyping of the GSTP1 rs1695 gene polymorphism was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Polymerase chain reaction (PCR) was used to perform genotyping of the GSTM1 and GSTT1 genes polymorphism.

RESULTS

There was a significant difference in genotype frequencies of the GSTP1 rs1695 gene polymorphism among the groups studied. The distribution of Val/Val genotype of the GSTP1 rs1695 gene polymorphism had a higher incidence in healthy workers compared with patients with toxic liver damage (p=0.036). No significant association was found between the GSTM1 and GSTT1 polymorphisms and toxic liver damage.

CONCLUSION

The GSTP1 rs1695 gene polymorphism can play a protective role in the development of toxic liver damage in petrochemical workers.

IGF1 polymorphisms and colon cancer risk in Tunisian population

BACKGROUND

Insuline-like growth factor I (IGF1) is a peptide growth factor that promotes cell proliferation and inhibits apoptosis.

AIM

To examine the association of genetic variants in IGF1 (rs12423791, rs1019731, rs5742632, rs2033178 and rs2373722) with risk of colon cancer in Tunisia.

METHODS

The study included 76 formalin-fixed paraffin embedded primary colorectal carcinomas and paired normal colon. The five IGF1 polymorphisms were determined by polymerase chain-restriction fragment length polymorphism (PCR-RFLP).

RESULT

A significant differences in genotypes and alleles frequency of the five examined IGF1 polymorphisms was determined between tumor and healthy tissues of colon cancer patients (P<0,01). While, no significant association was found between genetic variation in IGF1 variants and clinic-pathological parameters in tumors tissues. Expect for rs2373722, a statistically significant correlation was detected between tumor localization and the presence of the (A) mutated allele (OR=0,49; 95% CI 0,25-0,99; P=0,03).

CONCLUSION

This analysis shows that IGF1gene polymorphisms rs12423791, rs1019731, rs5742632, rs2033178 and rs2373722 are associated with the risk of colon cancer in Tunisian population.

Mannose-Binding Lectin Serum Level and Gene Polymorphism in Systemic Lupus Erythematosus Egyptian Patients

Systemic lupus erythematosus (SLE) is an autoimmune disease in which the complement system plays a role in its pathogenesis. Mannose-binding lectin (MBL) is a serum protein, being a component of innate immune system, it is responsible for lectin pathway of complement activation. The presence of several polymorphisms at the coding regions of the MBL-2 gene, especially single point mutation at codon 54, leads to decreased level and /or functional deficits of MBL, which seems to be a risk factor for occurrence of autoimmune diseases, such as in SLE. So, this study was carried out to determine the role of the serum MBL concentration and the genetic polymorphisms of MBL-2 gene exon 1 codon 54 in Egyptian patients with SLE. Forty-eight SLE patients and 48 matched healthy controls were investigated. MBL serum level was measured by ELISA technique. MBL-2 polymorphism at exon 1 codon 54 was determined by PCR-RFLP. Our results revealed a significant reduction in MBL serum level among SLE patient group in comparison to the control group (P < 0.001). MBL-2 genotyping among SLE patients, revealed the wild type (A/A) in 52.1% and mutant types (A/B, B/B) in 47.9%. While among healthy controls, the wild type was detected in 81.2% and the mutant types in 18.8% with a statistically significant association between this polymorphism and SLE susceptibility (P=0.008). Comparison of MBL serum level among different genotypes within the patient group showed that the mutant allele had a suppressive effect on MBL serum level. In conclusion, carrying MBL-2 exon-1 codon 54 variant allele B was shown to be a risk factor for SLE.

Molecular epidemiology and antifungal susceptibility profiles of clinical Cryptococcus neoformans/Cryptococcus gattii species complex

Introduction. Limited data regarding the epidemiology and susceptibility profiles of cryptococcosis are available in the Middle East.Aim. Our study aimed to evaluate the molecular diversity, mating types and antifungal susceptibility pattern of Cryptococcus species (n=14) isolated from 320 suspected patients with cryptococcosis.Methodology. The URA5 gene was subjected to restriction fragment length polymorphism and sequence analysis. In addition, in vitro antifungal susceptibility testing was performed by Clinical and Laboratory Standards Institute (CLSI) M27-A4 and M59 guidelines.Results. Overall, 14 (4.4 %) patients were confirmed as cryptococcosis. Based on molecular type, 85.7 and 14.3 % of the isolates were C. neoformans VN I and VN II, respectively. Phylogenetic analysis of URA5 gene sequences revealed clustering of VN I and VN II isolates into two distinct clades with a substantial difference within each molecular type. Voriconazole and 5-fluorocytosine, respectively, had the lowest (0.031 μg ml^-1) and highest (8 µg ml^-1) MICs. The epidemiological cutoff values (ECVs) for amphotericin B, fluconazole, voriconazole and 5-fluorocytosine encompassed ≥97 % of all 14 C. neoformans VN I species. However, according to the CLSI document M59, ECVs for itraconazole (7; 50 % of the isolates) and for posaconazole (1; 7.1 % of the isolate), were one log2 dilution higher than the wild type range. Combinations of amphotericin B with 5-fluorocytosine, amphotericin B with fluconazole and fluconazole with 5-fluorocytosine exhibited synergistic effects against 37, 31 and 12.5 % of the isolates, respectively.Conclusion. Our findings may significantly contribute to the development of management strategies for patients at a higher risk of cryptococcosis, particularly HIV-positive individuals.

Comparison between single and multi-locus approaches for specimen identification in Mytilus mussels

Mytilus mussels have been the object of much research given their sentinel role in coastal ecosystems and significant value as an aquaculture resource appreciated for both, its flavour and nutritional content. Some of the most-studied Mytilus species are M. edulis, M. galloprovincialis, M. chilensis and M. trossulus. As species identification based on morphological characteristics of Mytilus specimens is difficult, molecular markers are often used. Single-locus markers can give conflicting results when used independently; not all markers differentiate among all species, and the markers target genomic regions with different evolutionary histories. We evaluated the concordance between the PCR-RFLP markers most commonly-used for species identification in mussels within the Mytilus genus (Me15-16, ITS, mac-1, 16S rRNA and COI) when used alone (mono-locus approach) or together (multi-locus approach). In this study, multi-locus strategy outperformed the mono-locus methods, clearly identifying all four species and also showed similar specimen identification performance than a 49 SNPs panel. We hope that these findings will contribute to a better understanding of DNA marker-based analysis of Mytilus taxa. These results support the use of a multi-locus approach when studying this important marine resource, including research on food quality and safety, sustainable production and conservation.

Vitamin D receptor and binding protein polymorphisms in women with polycystic ovary syndrome: a case control study

BACKGROUND

Polycystic ovary syndrome (PCOS) is the most common endocrinopathy in women of reproductive age, characterized by hyperandrogenism, oligomenorrhea, polycystic ovary morphology, and insulin resistance. Vitamin D deficiency and vitamin D receptor (VDR)/vitamin D binding protein (VDBP) gene variants could play an important role in susceptibility to PCOS and contribute to metabolic disturbances and menstrual dysfunction. We aimed to investigate the associations of VDR gene and VDBP gene polymorphisms with PCOS susceptibility and to elucidate the impacts of these polymorphisms on the hormonal and metabolic parameters of PCOS.

METHODS

We recruited 432 women with PCOS and 927 controls. Polymorphisms in the VDR gene (VDR Fok-I, Cdx2, Apa-I, and Bsm-I) and VDBP gene (VDBP rs4588, rs7041, and rs22822679) were genotyped. A 75-g oral glucose tolerance test was performed.

RESULTS

The distributions of genotypes and allele frequencies in VDR and VDBP genes did not differ between PCOS and control. In women with PCOS, compared to the VDR Fok-I GG genotype, the VDR Fok-I AG genotype was significantly associated with increased levels of total testosterone (β = 5.537, P = 0.005). Compared to the VDR Cdx2 AC genotype, the VDR Cdx2 CC genotype was associated with increased levels of fasting insulin and HOMA-IR in women with PCOS, however, the associations were not statistically significant.

CONCLUSIONS

This finding indicates that genetic variations in VDR and VDBP were not associated with increased risk for PCOS. In contrast, the VDR Fok-I polymorphism was associated with testosterone level and the Cdx2 polymorphism with insulin sensitivity in PCOS. However, the Cdx2 polymorphism was not significantly associated with increased insulin and insulin sensitivity in women with PCOS after multiple linear regression.

Concordance of Giardia duodenalis assemblages determined by different PCR methodologies in three observational studies in Cuba

Giardia duodenalis is one of the most important intestinal parasites globally, especially in children, and in Cuba is the leading cause of chronic paediatric diarrhoea in this population. G. duodenalis is composed of eight genetic groups (or assemblages), two of which (A and B) are apparently zoonotic, occurring in both humans and other animals. However, consensus on the most appropriate genotyping scheme for optimal characterization of G. duodenalis isolates is lacking. In this article we present the results of three descriptive observational studies conducted in Havana, Cuba between 2010 and 2013, with the aim of comparing the results from molecular (PCR) approaches targeting different genes in order to assign with confidence 224 isolates of G. duodenalis to the correct assemblages. In each sub-study, following DNA isolation by the phenol/chloroform/isoamyl alcohol extraction method, PCR targeting the triose phosphate isomerase (tpi) gene was used for molecular characterization, as well as one additional PCR-method targeting another gene or pair of genes. DNA amplification was obtained in 87%, 83%, and 80% in the three sub-studies. Although excellent agreement (kappa index = 1) was recorded between results from some pairs of genes, for other combinations only moderate or substantial agreement was achieved. These results highlight the importance of interpretation of genotyping data, especially when single genetic markers are used. From the results of our studies, PCR targeting a combination of the tpi gene and the intergenic spacer region of rDNA may be a useful approach for the molecular characterization of G. duodenalis isolates.

Analysis of IL-4 promoter and VNTR polymorphisms in Thai patients with pulmonary tuberculosis

Tuberculosis (TB) is a leading cause of morbidity and mortality in Thailand. Cytokines play important roles in defense against Mycobacterium tuberculosis infection. Interleukin (IL)-4 is one of the anti-inflammatory cytokines and has been found to be elevated in TB patients. The common polymorphisms in IL-4 gene, including IL-4-590C/T, IL-4-33C/T, and IL-4-variable number of tandem repeats (VNTR) intron 3 have been reported to be associated with risk for some diseases. The purpose of this study was to investigate possible associations between the above mentioned three common functional polymorphisms in the IL-4 gene in patients with pulmonary tuberculosis (PTB) in a Thai population. Forty three patients with PTB and 90 healthy control subjects were studied. The three common polymorphisms of the IL-4 gene were determined using polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP). The allele and genotype frequencies of IL-4 -590 C/T, -33 C/T, VNTR intron 3 polymorphisms did not show significant differences between PTB patients and healthy controls (genotype: p=0.88, p=0.92, p=0.40; allele: p=0.38, p=0.44, p=0.53, respectively). However, the allele distribution of the IL-4 -590 C, -33 C, and VNTR R3 was higher among PTB patients (25.58%, 25.58%, 25.58%, respectively) than among control subjects (20%, 20.48%, 19.44%, respectively). This may suggest that IL-4-590C/T, -33C/T and VNTR intron 3 might play a role in susceptibility to PTB. A larger cohort may possibly help conclude our findings.

High Seroprevalence but Low Rate of Isolation of Toxoplasma gondii from Wild Elk (Cervus Canadensis) in Pennsylvania

Toxoplasma gondii infections are prevalent in most warm-blooded animals worldwide. During the 2018 November hunting season in Pennsylvania, fresh (unfixed, not frozen) samples obtained from 99 harvested elk (Cervus canadensis) were tested for T. gondii infection. Antibodies to T. gondii were detected in 69 of 99 (69.7%) elk tested by the modified agglutination test (MAT, 1:25 cut-off). Tongues and hearts from 16 elk with high MAT titers (>1:200) were bioassayed for T. gondii by inoculation in outbred Swiss Webster (SW) and interferon-gamma gene knockout (KO) mice. Viable T. gondii was isolated from tongues of 2 elk with MAT titers of 1:200 and 1:3,200. Toxoplasma gondii from both isolates were successfully propagated in cell culture. Genetic typing on DNA extracted from culture-derived tachyzoites using the PCR restriction fragment length polymorphism with 10 genetic markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico) revealed that both isolates belonged to ToxoDB PCR-RFLP genotype #5 that is widely prevalent in wildlife in the United States. Our results suggest that elk may clear T. gondii organisms from their tissues.

Analysis of Mycobacterium tuberculosis genetic lineages circulating in Riga and Riga region, Latvia, isolated between 2008 and 2012

Although the number of new tuberculosis (TB) cases registered per year has decreased by 3-fold between 2001 and 2017 in Latvia, the TB incidence and rates of multidrug resistant TB in this Baltic country remain substantially higher than in most other European countries. Molecular typing methods of Mycobacterium tuberculosis (MTB) play an important role both in clinical studies of the disease and the epidemiological investigations, allowing to describe and characterize the pathogen's population structure and spread of particular genotypes. Aim of this study was to examine the prevalence of MTB lineages in Riga and Riga region of Latvia within a five-year period (2008-2012), and to evaluate the discriminatory power (DP) of spoligotyping, standard 24-locus MIRU-VNTR and IS6110-RFLP methods in this setting. The results showed that the main MTB spoligotype families were Beijing (25.3%) and LAM (24.3%), followed by T (22.1%), Ural (11.2%), Haarlem (6.6%) and X superfamily (3.4%). This distribution remained stable over the five consecutive years. 67.6% of MTB isolates were pan-susceptible, and 32.4% were resistant to any drug; multi-drug resistance was found in 5.8% of MTB strains, and 7.6% of MTB isolates were extensively drug-resistant. Drug resistance was associated with SIT1, SIT283 and SIT42 genotypes, while SIT1 and SIT42 were overrepresented among multi drug-resistant MTB strains. Overall, DP of spoligotyping method alone was 0.8953, while DP of both 24-locus MIRU-VNTR analysis and IS6110 RFLP was higher (DP = 0.9846 and 0.9927, respectively), mainly due to the improvement of the resolution for the Beijing strains. In conclusion, this work represents the first comprehensive molecular epidemiological description of TB in Latvia, highlighting the high genetic diversity of MTB strains circulating in Riga and Riga region. In combination with detailed epidemiological data this approach was helpful for the in-depth understanding of epidemiological processes in settings where the Next-Gen sequencing is not available as a routine method.

Geospatial analysis of tegumentary leishmaniasis in Rio de Janeiro state, Brazil from 2000 to 2015: Species typing and flow of travelers and migrants with leishmaniasis

Background

We identified the species of Leishmania isolated from traveling and migrant patients attended in a reference center from 2000 to 2015, we performed the georeferencing of these species in Rio de Janeiro (RJ) state and we had knowledge about the human flows between the likely location of infection (LLI) and place of residence (PR) in RJ state, Brazil.

Methodology/Principal findings

This is a retrospective cross-sectional study including 171 patients diagnosed with ATL. Google Maps, OpenStreetMap, and Bing Maps were tools used to georeference LLI and PR. For etiological identification, we used isoenzyme electrophoresis, polymerase chain reaction-restriction fragment length polymorphism (molecular target hsp70C with restriction enzymes HaeIII and BstUI), and sequencing of the internal transcribed spacer of ribosomal DNA. ARCGIS software was used to create maps of the geographic distribution of Leishmania species in the state and municipality of RJ, together with flows between the LLI and PR. Isolates from 104 patients were identified as: L. (Viannia) braziliensis (80.8%), L. (V.) naiffi (7.7%), L. (V.) guyanensis (6.7%), L. (Leishmania) amazonensis (1%), and genetic variants of L. (V.) braziliensis (3.8%). The flow maps showed that the LLI included 4 countries, 19 Brazilian states, and 18 municipalities of RJ state. The Brazilian states with the highest density of cases were Amazonas (n = 32), Bahia (n = 18), and Ceará (n = 15).

Conclusions/Significance

This work is the first contribution to the knowledge of the routes of Leishmania species introduced in RJ state by migrants and travelers patients. L. (V.) braziliensis, L. (V.) guyanensis, L. (V.) naiffi, L. (L.) amazonensis, and genetic variants of L. (V.) braziliensis were identified in RJ state. To determine whether the autochthonous transmission of these imported species is possible it is necessary the adaptation of these species to environmental conditions as well as the presence of reservoirs and phlebotomine vectors in this region.

Leishmaniasis is one of the most important neglected parasitic diseases in humans worldwide. American Tegumentary Leishmaniasis (ATL) is a disease caused by protozoa of the genus Leishmania, which are injected into the skin by small insects known by sandflies. Many different Leishmania species may cause ATL, which can affect the skin and/or oral and nasal mucosa. In this study, we analyzed flows between the likely location of infection (LLI) and the place of residence (PR) in Rio de Janeiro (RJ) state and identified Leishmania species isolated from travelers and migrants attended between 2000 and 2015 in a reference hospital for the care of patients with ATL. This work is the first contribution to knowledge about the routes of Leishmania species introduced to RJ state by migrant and traveling patients. In addition to Leishmania (Viannia) braziliensis, which was the most common species, other species have also been introduced to RJ state, including L. (V.) guyanensis, L. (V.) naiffi, L. (Leishmania) amazonensis, and genetic variants of L. (V.) braziliensis. Knowledge of the migratory flow and geographic location of these imported Leishmania species may contribute to the surveillance and control of ATL in RJ state, Brazil.

Newborn Screening for Spinal Muscular Atrophy: DNA Preparation from Dried Blood Spot and DNA Polymerase Selection in PCR

BACKGROUND

Polymerase chain reaction (PCR) analysis using DNA from dried blood spot (DBS) samples on filter paper is a critical technique for spinal muscular atrophy (SMA) newborn screening. However, DNA extraction from DBS is time-consuming, and elimination of PCR inhibitors from DBS is almost impossible.

METHODS

Exon 7 of the two homologous SMA-related genes, survival motor neuron (SMN) 1 and SMN2, of five SMA patients and five controls were amplified by PCR with a punched-out circle of the DBS paper. Two types of DNA preparation methods were tested; DNA-extraction (extracted DNA was added in a PCR tube) and non-DNA-extraction (a punched-out DBS circle was placed in a PCR tube). As for the DNA polymerases, two different enzymes were compared; TaKaRa Ex Taq™ and KOD FX Neo™. To test the diagnostic quality of PCR products, RFLP (Restriction fragment length polymorphism) analysis with DraI digestion was performed, differentiating SMN1 and SMN2.

RESULTS

In PCR using extracted DNA, sufficient amplification was achieved with TaKaRa Ex Taq™ and KOD FX Neo™, and there was no significant difference in amplification efficiency between them. In direct PCR with a punched-out DBS circle, sufficient amplification was achieved when KOD FX Neo™ polymerase was used, while there was no amplification with TaKaRa Ex Taq™. RFLP analysis of the direct PCR products with KOD FX Neo™ clearly separated SMN1 and SMN2 sequences and proved the presence of both of SMN1 and SMN2 in controls, and only SMN2 in SMA patients, suggesting that the direct PCR products with KOD FX Neo™ were of sufficient diagnostic quality for SMA testing.

CONCLUSION

Direct PCR with DNA polymerases like KOD FX NeoTM has potential to be widely used in SMA newborn screening in the near future as it obviates the DNA extraction process from DBS and can precisely amplify the target sequences in spite of the presence of PCR inhibitors.

In silico design and in vitro validation of a novel PCR-RFLP assay for determination of phylogenetic clusters of streptokinase gene alleles in streptococci groups

Streptokinase (SK), a heterogeneous plasminogen (Pg) activator protein secreted by groups A, C and G streptococci (GAS/GCS/GGS) is a virulence factor composed of three structural domains; SKα/SKβ/SKγ. Phylogenetic analysis of the major variable region of SKβ (sk-V1; nucleotides 448-791; 343bp) which classifies the SK alleles into SK1/SK2 clusters and SK2a/SK2b sub-clusters, is an approved assay to categorize clinical/natural streptococcal-isolates into co-related functional/pathogenesis groups. Herein, we describe a novel PCR-RFLP assay that in combination with Numerical Taxonomy and multivariate analysis System (NTSYS) resulted to dendrograms with complete adaption to that of the phylogenetic analysis of sk-V1-based clustering. In silico analyses by 30 restriction enzymes on GenBank-acquired sk-V1 sequences of known streptococcal clusters, resulted to the selection of "BsrI, MseI and Tsp45I″ enzymes that produced proper patterns to construct the expected dendrograms. In vitro analysis of the selected enzymes on clinical isolates of GAS/GCS/GGS validated the production of the same in silico-observed digestion patterns. Comparison of the constructed dendrogram and phylogenetic trees of selected GenBank and clinical isolates of streptococci indicated complete adaptation. Assessment of Pg-activation activity in selected clinical isolates indicated the expected co-related functionalities of the classified SK-clusters by the invented PCR-RFLP/NTSYS method. The simplicity of the assay relieves the need of sequencing/phylogenetic analyses for SK-clustering.

Association between interleukin-8 gene -251 A/T polymorphism and the risk of coronary artery disease: A meta-analysis

BACKGROUND

The association between interleukin-8 (IL-8) gene polymorphism -251 A>T and susceptibility to coronary artery disease (CAD) has been investigated previously; however, results remain controversial. Thus, a meta-analysis was conducted to reassess the effects of this polymorphism on CAD risks.

METHODS

The PubMed, Cochrane Library, China National Knowledge Infrastructure, and Wanfang databases were searched for relevant studies published up to December, 2018. The pooled odds ratios (OR) were calculated using STATA 13.0 software for allelic (A vs T) as well as homozygote (AA vs TT), heterozygote (AT vs TT), recessive (AA vs AT + TT), and dominant (AA + AT vs TT) genotype models, respectively.

RESULTS

Ten case-control studies (3744 cases and 3660 controls) were included. Overall, a significant association of IL-8 gene -251 A > T polymorphism with an increased risk of CAD was only observed in the dominant genotype model (OR = 1.48), but not others. In the subgroup analysis, significantly increased risks were also found for Chinese (OR = 1.64), polymerase chain reaction-restriction fragment length polymorphism genotyping (OR = 1.61), acute coronary syndrome (ACS) type (OR = 1.92 for 3 datasets; OR = 1.88 for 4 datasets), high quality (OR = 1.64), and age/gender matching status (OR = 1.55) under the dominant model. Furthermore, significantly increased risks were also found for ACS type under allelic (OR = 1.32 for 3 datasets; OR = 127 for 4 datasets), homozygote (OR = 1.64 for 3 datasets; OR = 1.50 for 4 datasets), heterozygote (OR = 1.32 for 3 datasets; OR = 1.30 for 4 datasets), and recessive (OR = 1.40 for 3 datasets; OR = 1.28 for 4 datasets) models.

CONCLUSION

This meta-analysis suggests that Chinese patients carrying -251A allele of IL-8 may have an increased risk for the development of CAD, especially ACS.

Inter- and intra-genotype differences in induced cystogenesis of recombinant strains of Toxoplasma gondii isolated from chicken and pigs

The ability to differentiate from the proliferative (tachyzoite) to the latent (bradyzoite) stage of isolates of Toxoplasma gondii recombinant genotypes (I/II/III and I/III) and reference strains from a clonal line (RH and ME49) was investigated in this study. Two isolates from chicken (#114 and #277; ToxoDB) and 3 from pigs (#114; ToxoDB) were the subjects for evaluation. The isolates were grown in cell culture under 2 different conditions: culture medium at pH 7.0 (neutral, without stress induction) or pH 8.0 (alkaline, stress inducing). After 4 days, the cultures were fixed and the events resulting from infection and induction were labeled. T. gondii cysts were labeled using Dolichos biflorus-FITC lectin (DBL-cysts) and free tachyzoites or vacuolar were labeled using an anti-T. gondii polyclonal antibody followed by an Alexa 594-conjugated secondary antibody (DBL-negative structures compatible with parasite structures - lysis plaques or vacuole). Differences in DBL-cysts formation in vitro in response to exogenous stress were observed between recombinant genotype isolates and the typical genotypes. The differences in conversion rates and the patterns of lysis plate production between genotype I/III isolates (#114) indicate that care should be taken when extrapolating the in vitro phenotypic characteristics of parasites from the same genotype.

Association of Phlebotomus guggisbergi with Leishmania major and Leishmania tropica in a complex transmission setting for cutaneous leishmaniasis in Gilgil, Nakuru county, Kenya

BACKGROUND

Phlebotomus (Larroussius) guggisbergi is among the confirmed vectors for cutaneous leishmaniasis (CL) transmission in Kenya. This scarring and stigmatizing form of leishmaniasis accounts for over one million annual cases worldwide. Most recent CL epidemics in Kenya have been reported in Gilgil, Nakuru County, where the disease has become a public health issue. However, little is known about the factors that drive its transmission. Here, we sought to determine the occurrence, distribution and host blood feeding preference of the vectors, and to identify Leishmania species and infection rates in sandflies using molecular techniques. This information could lead to a better understanding of the disease transmission and improvement of control strategies in the area.

METHODOLOGY/ PRINCIPAL FINDINGS

An entomological survey of sandflies using CDC light traps was conducted for one week per month in April 2016, and in June and July 2017 from five villages of Gilgil, Nakuru county; Jaica, Sogonoi, Utut, Gitare and Njeru. Sandflies were identified to species level using morphological keys and further verified by PCR analysis of cytochrome c oxidase subunit I (COI) gene. Midguts of female sandflies found to harbour Leishmania were ruptured and the isolated parasites cultured in Novy-MacNeal-Nicolle (NNN) media overlaid with Schneider's insect media to identify the species. Leishmania parasite screening and identification in 198 randomly selected Phlebotomus females and parasite cultures was done by PCR-RFLP analysis of ITS1 gene, nested kDNA-PCR and real-time PCR-HRM followed by sequencing. Bloodmeal source identification was done by real-time PCR-HRM of the vertebrate cytochrome-b gene. A total of 729 sandflies (males: n = 310; females: n = 419) were collected from Utut (36.6%), Jaica (24.3%), Sogonoi (34.4%), Njeru (4.5%), and Gitare (0.1%). These were found to consist of nine species: three Phlebotomus spp. and six Sergentomyia spp. Ph. guggisbergi was the most abundant species (75.4%, n = 550) followed by Ph. saevus sensu lato (11.3%, n = 82). Sandfly species distribution across the villages was found to be significantly different (p<0.001) with Jaica recording the highest diversity. The overall Leishmania infection rate in sandflies was estimated at 7.07% (14/198). Infection rates in Ph. guggisbergi and Ph. saevus s.l. were 9.09% (12/132) and 3.57% (2/56) respectively. L. tropica was found to be the predominant parasite in Gilgil with an overall infection rate of 6.91% (13/188) in Ph. guggisbergi (n = 11) and Ph. saevus s.l. (n = 2) sandflies. However, PCR analysis also revealed L. major infection in one Ph. guggisbergi specimen. Bloodmeal analysis in the 74 blood-fed sandflies disclosed a diverse range of vertebrate hosts in Ph. guggisbergi bloodmeals, while Ph. saevus s.l. fed mainly on humans.

CONCLUSIONS/ SIGNIFICANCE

The high infection rates of L. tropica and abundance of Ph. guggisbergi in this study confirms this sandfly as a vector of L. tropica in Kenya. Furthermore, isolation of live L. tropica parasites from Ph. saevus s.l. suggest that there are at least three potential vectors of this parasite species in Gilgil; Ph. guggisbergi, Ph. aculeatus and Ph. saevus s.l. Molecular identification of L. major infections in Ph. guggisbergi suggested this sandfly species as a potential permissive vector of L. major, which needs to be investigated further. Sandfly host preference analysis revealed the possibility of zoonotic transmissions of L. tropica in Gilgil since the main vector (Ph. guggisbergi) does not feed exclusively on humans but also other vertebrate species. Further investigations are needed to determine the potential role of these vertebrate species in L. tropica and L. major transmission in the area.

Genetic association between cluster of differentiation 86 variations and sepsis risk: A case-control study

The aim of this study was to investigate the correlation between cluster of differentiation 86 (CD86) gene rs1129055 and rs2715267 single nucleotide polymorphisms and sepsis susceptibility.One hundred twenty-five sepsis patients and 120 healthy controls were enrolled in this case-control study. CD86 polymorphisms rs1129055 and rs2715267 were genotyped through polymerase chain reaction-restriction fragment length polymorphism approach. Chi-square test was used to analyze differences in genotype and allele frequencies of the 2 polymorphisms between case and control groups. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to present the association strength of the polymorphisms with sepsis susceptibility.AA genotype and A allele frequencies of CD86 rs1129055 were significantly lower in sepsis patients than in healthy controls (P < .05), revealing their significant associations with decreased disease susceptibility (OR = 0.351, 95% CI = 0.169-0.728; OR = 0.593, 95% CI = 0.415-0.847). Nevertheless, rs2715267 had no significant association with sepsis susceptibility (P > .05).AA genotype and A allele of CD86 polymorphism rs1129055 might be correlated with decreased sepsis susceptibility in Chinese Han population, but not rs2715267. Further study should be performed to verify our findings.

Distribution of polymorphism rs693 of ApoB gene in a sample of Colombian Caribbeans

INTRODUCTION

Several studies have reported that the single nucleotide polymorphism rs693 of Apo lipoprotein B gene is associated with high levels of plasma lipids and high body mass index, which are risk factors for cardiovascular diseases. The distribution of this single nucleotide polymorphism and its association with the phenotype depend on the genetic background of each population.

OBJECTIVE

To evaluate the distribution of single nucleotide polymorphism rs693 and its association with lipid profile and body mass index in a sample of Colombian Caribbeans.

METHODS

108 non-related adult subjects of both gender were included in this study. Body mass index and lipid profile that included total cholesterol, triglycerides, Low Density Lipoprotein and High Density Lipoprotein were determined. The single nucleotide polymorphism rs693 was determined by Polymerase Chain Reaction/Restriction Fragment Length Polymorphism from genomic DNA followed by digestion with the restriction enzyme XbaI. The chi-square test was used to analyze the genotype distribution of rs693 and the genotype-phenotype association was evaluated through different inheritance model.

RESULTS

The genotype frequencies for single nucleotide polymorphism rs693 were CC (45.0%), TT (16.5%) and CT (38.5%). The allele frequencies were C (64.0%) and T (36.0%). The single nucleotide polymorphism was in Hardy-Weinberg equilibrium in the studied sample. No association of the single nucleotide polymorphism rs693 with lipid profile nor the body mass index was found (p >0.05).

CONCLUSION

There is no significant association between single nucleotide polymorphism rs693 and body mass index nor lipid profile, in a sample of Colombian Caribbeans.

Possible synergistic effect of apoE and LRP1 genotypes on metabolic syndrome development in Serbian patients

The modern way of life contributes to the higher frequency of a complex state medically called metabolic syndrome (MetS), which is an inevitable consequence of several most common diseases of modern civilization. Patients with MetS have three times higher risk of experiencing a heart attack or a stroke and twice higher possibility to die from them. Serbia holds the infamous third place in Europe in mortality from heart disease, just behind Russia and Ukraine. The study explores the correlation of every combination of genotypes of apoE (apolipoprotein E) and LRP1 (low density receptor- related protein 1) genes with presence of MetS, and the connection with each anthropometric and biochemical parameter in both tested groups. Study demonstrates the impact of genotype combinations on the emergence and development of the MetS in Serbia. 63 patients and 30 controls were included in the study, aged from 19 to 65. Each person genotype was determined by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) profile. Odds ratio (OR) values showed that the presence of apoE e3e4/LRP1 CC genotype combination of genotypes in patients multiplies the chance (7.6 times) for the occurrence of the MetS in comparison to the presence of other genotype combinations. Determining the genetic basis of MetS is one of the necessary steps in the prevention of disease, saving the cost of treatment, and in the design of targeted therapies.

The Relationship Between Urothelial Type Bladder Cancer, Plasma 25-Hydroxyvitamin D Levels, and Vitamin D Receptor ApaI BsmI FokI, and TaqI Polymorphisms

BACKGROUND

Bladder cancer is an important health problem which ranks 4th among most frequently seen cancer types in men. In our study we aimed to investigate the correlations among urothelial type bladder cancer polymorphisms, ApaI, BsmI, FokI, and TaqI, prevalently observed in the vitamin D receptor (VDR) gene and plasma vitamin D levels in a Turkish population.

METHODS

Our study included 101 patients and 109 control subjects. Plasma 25(OH)D levels were determined using a HPLC method and VDR gene polymorphisms with PCR-RFLP method.

RESULTS

A statistically significant intergroup difference was not observed with regard to age, gender, and BMIs of the patients. Median (min - max) 25(OH)D levels in the patient and the control groups were determined as 11.9 ng/dL (1.9 - 33.0 ng/dL) and 9.7 ng/dL (2.1 - 39.5 ng/dL), respectively. A statistically significant intergroup difference was not observed with regard to 25(OH)D levels (p = 0.402). A statistically significant intergroup differ-ence was not observed with regard to genotype distribution of ApaI, BsmI, and TaqI polymorphisms and allele frequencies. Control and urothelial type bladder cancer groups showed a statistically significant difference with respect to genotype distribution of FokI polymorphism (p = 0.048). However in a binary logistic regression model, when corrected OR values were estimated by including smoking history in the model, the correlation detected be-tween the presence of FF and increased risk of disease was not statistically significant (ORadj = 1.64, 95% CI = 0.89 - 3.02, p = 0.114).

CONCLUSIONS

In the light of the data concerning Turkish population a statistically significant correlation could not be demonstrated between plasma vitamin D levels, ApaI, BsmI, FokI, and TaqI polymorphisms, and urothelial type bladder cancers. Since literature data are limited in number, further studies should be conducted in larger patient groups.

The rs1986112 Variant is Associated with Increased RAB8B Gene Expression in Schizophrenic Patients

BACKGROUND

Schizophrenia (SCZ) is a serious mental disorder that interferes with a person's cognitive processes and leads to social disability. A wide range of factors may play important roles in increased risk of SCZ development. Genetic contributors are among the most influential actors involved in different molecular mechanisms leading to the development of the nervous system, thus they play pivotal roles in psychotic disorders and SCZ de-velopment. RAB8B is characterized for its key roles in several cellular and molecular mechanisms which are linked with different psychotic disorders, such as SCZ.

METHODS

In this study, we assessed the expression level of RAB8B gene in blood samples of schizophrenic patients and normal healthy controls by means of quantitative real time PCR. We also investigated the correlation between RAB8B-rs1986112 genotypes and RAB8B expression levels through SNP genotyping by means of the PCR-RFLP method.

RESULTS

Our results indicated a significant difference of RAB8B mRNA ratio between SCZ patients and healthy controls. Moreover, we showed significant upregulation of RAB8B in patients with rs1986112 GG and AG genotype compared to AA genotype.

CONCLUSIONS

Our findings suggest a role for RAB8B and its regulatory variation, rs1986112 in SCZ development.

The Prevalence of Mixed Genotype Infections in Turkish Patients with Hepatitis C: a Multicentered Assessment

BACKGROUND

HCV virus infections are one of the major health problems in the world that can cause cirrhosis and liver cancer at a higher rate than other hepatitis data. The aim of this study was to determine the prevalence of mixed infections with different HCV genotypes in Turkey and also to evaluate the current HCV genotype and sub-type distributions by a multicentered assessment.

METHODS

The HCV genotype data of 17,578 hepatitis C patients collected from 23 centers from different geographic regions covering all Turkey were collected. The data included information about the HCV genotypes in the last 10 years (between 2007 and 2016), demographic properties of the patients and the methods/systems used to determine the genotypes.

RESULTS

Two hundred twenty-eight of the patients (1.3%) had mixed genotype. The most common mixed genotype combination was 1b + 4 (0.83%) followed by 1a + 1b (0.26%). Genotype distribution varies according to geographical regions. However, genotype 1 (82.92%) was the most common genotype in all regions and all years. This was followed by genotype 3 (7.07%) and genotype 4 (5.43%). A variety of methods were used by the centers including sequencing, pyrosequencing, real-time PCR, in-house RFLP, reverse hybridization (LIPA), and hybridization.

CONCLUSIONS

Infection with mixed HCV genotypes in Turkey is uncommon. Genotype distribution varies according to geographic regions; the most common genotype 1 is encountered all over the country, while genotypes 3 and 4 are only in some of the centers. Since there is limited information about mixed HCV infection, further investigations are needed to determine the clinical importance of mixed HCV infection.

Can the genetic polymorphisms of the folate metabolism have an influence in the polycystic ovary syndrome?

OBJECTIVE

To investigate the association of the genetic variants of the folate metabolism genes (MTHFR C677T; MTHFR A1298C; MTR A2756G; MTRR A66G and RFC-1 A80G) with the development of polycystic ovary syndrome (PCOS).

SUBJECTS AND METHODS

This study included 203 women (99 women with PCOS and 104 controls). The genotyping was performed by PCR-RFLP. Chi-squared test and multiple logistic regression were used in the statistical analysis. Haplotype analysis was conducted using the SNPstat program. The results were presented in odds ratio (OR) and confidence interval of 95% (CI-95%), with a significance level of 5% (p ≤ 0.05).

RESULTS

The genotypic distribution of the RFC-1 A80G polymorphism showed significant difference between the two groups, showing that the heterozygous genotype (AG genotype) was most frequent in controls. The polymorphic homozygous (GG genotype) of MTRR A66G polymorphism were most frequent in controls. The T-C haplotype MTHFR C677T and A1298C polymorphisms were more frequent in the control group (OR = 0.19; CI 95% - 0.04 to 0.93 e p = 0.042). The multivariate analysis evidenced that family history of PCOS was more frequent in the PCOS group (OR = 3.29; CI 95% - 1.48 to 7.31; p = 0.003).

CONCLUSION

In our casuistry, the polymorphic homozygous of MTRR A66G polymorphism gene and heterozygous of RFC-1 A80G polymorphism gene, the haplotype T-C C677T and A1298C polymorphisms of MTHFR gene, can be associated with protective factors for the disease.

A Variation in the ABCC8 Gene Is Associated with Type 2 Diabetes Mellitus and Repaglinide Efficacy in Chinese Type 2 Diabetes Mellitus Patients

Objective Previous studies have suggested that variations in the ABCC8 gene may be closely associated with T2DM susceptibility and repaglinide response. However, these results have not been entirely consistent, and there are no related studies in a Chinese population, suggesting the need for further exploration. The current study investigated the associations of the ABCC8 rs1801261 polymorphism with type 2 diabetes mellitus (T2DM) susceptibility and repaglinide therapeutic efficacy in Chinese Han T2DM patients. Methods A total of 234 T2DM patients and 105 healthy subjects were genotyped for ABCC8 rs1801261 polymorphism by a polymerase chain reaction-restriction fragment length polymorphism assay. A total of 70 patients with the same genotypes of CYP2C8*3 139Arg and OATP1B1 521TT were randomized to orally take 3 mg repaglinide per day (1 mg each time before meals) for 8 consecutive weeks. The pharmacodynamic parameters of repaglinide and biochemical indicators were then determined before and after repaglinide treatment. Results The frequency of ABCC8 rs1801261 allele was higher in T2DM patients than in the control subjects (22.6% vs.11.0%, p<0.01). After repaglinide treatment, T2DM patients carrying genotype CT showed a significantly attenuated efficacy on FPG (p<0.01) and HbA1c (p<0.01) compared with those with genotype CC. Conclusion These results suggested that the ABCC8 rs1801261 polymorphism might influence T2DM susceptibility and the therapeutic effect of repaglinide in Chinese Han T2DM patients. This study was registered in the Chinese Clinical Trial Register on May 14, 2013 (No. ChiCTR-CCC13003536).

Association of endothelial nitric oxide synthase (eNOS) and norepinephrine transporter (NET) genes polymorphism with type 2 diabetes mellitus

Genetic factors in combination with environmental factors play a critical role in the development type 2 diabetes mellitus (T2DM) which is growing as an epidemic globally. In present study we aim to assess the association of eNOS (G894T, rs1799983) and NET (G1287A, rs5569) genes polymorphism with T2DM. A case-control study including a total of 400 North Indian subjects (200 T2DM cases and 200 controls) was performed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach to analyze genetic polymorphism. Alleles/genotype frequencies between cases and controls were compared using χ² and Student's t-tests. Odds ratios and 95% confidence intervals were calculated by logistic regression to assess the relative association between disease and genotypes. In case of NET gene, GG (P = 0.002 in T2DM males, 0.053 in overall T2DM cases) genotype and G allele (P = 0.003 in T2DM males, 0.027 in overall T2DM cases) were found to be a positive risk factors and AG genotype (P = 0.012 in T2DM males) and A allele (P = 0.003 in T2DM males, P = 0.027 in overall T2DM cases) as negative risk factor for T2DM. No association of eNOS gene polymorphism was found with T2DM (P values of all genotypes and alleles were greater than 0.05). NET gene polymorphism might be associated with the risk of T2DM whereas; eNOS gene polymorphism do not confer any risk of T2DM in North Indian Ethnic group. It is hoped that understanding genetic causes of T2DM will lead to earlier diagnosis, preventive measures and more effective and specific treatment.

Generalized glycogenosis in Brahman-derived breeds: diagnosis and prevalence in Argentina

Generalized glycogenosis is a lethal autosomal recessive disease caused by a deficient activity of the acidic 1,4-α-glucosidase enzyme and characterized by an accumulation of glycogen within lysosomes. Three mutations in the GAA gene causing bovine generalized glycogenosis have been identified in two cattle breeds, Brahman and Shorthorn. The objective of this study was to evaluate the prevalence of carriers of the E7 mutation in the GAA gene in Argentinean Brahman-derived herds. A total of 930 Braford, 94 Brangus, and 8 Brahman samples were analyzed. The genotyping was done by polymerase chain reaction and restriction fragment length polymorphism (PCR/RFLP). We found that 12.02% (95% CI 12.00-12.04) of the total number of samples received were heterozygous (i.e., carriers) for the E7 mutation, while 12.58% (95% CI 12.56-12.60) of the Braford, 6.38% (95% CI 6.26-6.51) of the Brangus, and 12.50% (95% CI 9.82-15.18) of the Brahman samples were carriers of this loss-of-function allele. Neither breed nor sex were significantly associated to the presence of the mutation. The prevalence informed in this study is similar to the average prevalence reported for Australian Brahmans. The finding of heterozygous animals suggests that breeders and insemination centers should continue screening their herds to minimize the dissemination of this deleterious allele.

Association between vitamin D receptor gene polymorphisms and Graves' disease: a systematic review and meta-analysis

PURPOSE

The pathogenesis of Graves' disease (GD) and orbitopathy (GO) is not completely elucidated. On the other hand, vitamin D receptor (VDR) gene polymorphisms have been associated with vulnerability to a plethora of chronic autoimmune diseases. The primary aim of this study was to synthesize evidence on the association between VDR gene polymorphisms and GD. Secondary aim was to investigate their association with GO.

METHODS

A comprehensive search was conducted in PubMed, CENTRAL and Scopus, up to December 8, 2018. Data were expressed as odds ratio (OR) with 95% confidence intervals (CI). Heterogeneity was quantified with I² index.

RESULTS

Ten studies were included in the qualitative and quantitative analysis. TT subtype of TaqI polymorphism was associated with an increased risk of GD compared with Tt and tt polymorphisms (OR: 1.42; 95% CI, 1.05-1.94, p = 0.025), whereas tt was associated with a lower risk of GD, compared with TT and Tt polymorphisms (OR: 0.79; 95% CI, 0.62-0.99, p = 0.043). No association was found for ApaI, BsmI, and FokI polymorphisms. The bb subtype of BsmI polymorphism was associated with a lower risk in Asian, but with a higher GD risk in Caucasian populations, compared with BB/Bb subtypes. No eligible study was found regarding the association between VDR gene polymorphisms and the risk of GO.

CONCLUSIONS

The TT subtype of the TaqI polymorphism was associated with a higher susceptibility for GD compared with Tt and tt. Regarding BsmI, the bb subtype was associated with increased GD risk in Caucasians, whereas it is protective in Asians.

Epidemiology of Clostridioides difficile infections, France, 2010 to 2017

BackgroundClostridioides difficile is a leading cause of healthcare-associated diarrhoea in middle and high-income countries. Up to 2018, there has been no systematic, annual surveillance for C. difficile infections (CDI) in France.AimsTo provide an updated overview of the epidemiology of CDI in France between 2010 and 2017 based on five different data sources.MethodsThis is a descriptive study of retrospective surveillance and alerts data. Incidence of CDI cases was estimated through the CDI incidence survey (2016) and data from the French National Uniform Hospital Discharge Database (PMSI; 2010-16). Testing frequency for CDI was estimated through the CDI incidence survey and point prevalence studies on healthcare-associated infections (HAI; 2012 and 2017). The national early warning response system for HAI (HAI-EWRS, 2012-17) and National Reference Laboratory data (2012-17) were used to follow the number of severe CDI cases and/or outbreaks.ResultsIn 2016, CDI incidence in acute care was 3.6 cases per 10,000 patient days (PD). There was a statistically significant increase in CDI incidence between 2010 and 2016 (+ 14% annually) and testing frequency was 47.4 per 10,000 PD. The number of CDI HAI-EWRS notifications decreased between 2015 and 2017 with only a few large outbreaks reported.ConclusionThe CDI incidence estimate increased from 2010, but remained below the European average of 7 per 10,000 PD in 2014; there were fewer severe cases or clusters reported in France. The consistency between PMSI and laboratory-based estimated CDI incidence could allow for more routine monitoring of CDI incidence.

Spinal Muscular Atrophy: Advanced Version of Screening System with Real-Time mCOP-PCR and PCR-RFLP for SMN1 Deletion

BACKGROUND

Spinal Muscular Atrophy (SMA) is a common autosomal recessive neuromuscular disease characterized by defects of lower motor neurons. More than 95% of SMA patients show homozygous deletion for the survival motor neuron 1 (SMN1) gene. For the screening of SMN1 deletion using dried blood spot (DBS), we developed a new combined system with real-time "modified competitive oligonucleotide priming"-polymerase chain reaction (mCOP-PCR) and PCR restriction fragment length polymorphism (PCR-RFLP). Although our real-time mCOP-PCR method is secured enough to be gene-specific, its amplification efficiency is not as good because the reverse primers carry a nucleotide mismatched with the sequence of the pre-amplified product. The mismatch has consequently been generated in the process of introducing a restriction enzyme site in the pre-amplified products for PCR-RFLP.

METHOD

DBS samples of the subjects were stored at room temperature for a period of less than one year. Each subject had already been genotyped by the first PCR-RFLP using fresh blood DNA. SMN1/SMN2 exon 7 was collectively amplified using conventional PCR (targeted pre-amplification). Pre-amplified products were used as template in the real-time mCOP-PCR, and, on the other hand, were digested with DraI enzyme (PCR-RFLP). To improve the amplification efficiency of mCOP-PCR, one nucleotide change was introduced in the original reverse primers (SMN1-COP and SMN2-COP) to eliminate the mismatched nucleotide.

RESULTS

The real-time mCOP-PCR with a new primer (SMN1-COP-DRA or SMN2-COP-DRA) more rapidly and specifically amplified SMN1 and SMN2, and clearly demonstrated SMN1 deletion in an SMA patient. With the new primers, the amplification efficiencies of real-time mCOP-PCR were improved and the Cq values of SMN1 (+) and SMN2 (+) samples were significantly lowered.

CONCLUSION

In the advanced version of our screening system for homozygous SMN1 deletion using DBS, the real-time mCOP-PCR with newly-designed reverse primers demonstrated the presence or absence of SMN1 and SMN2 within a shorter time, and the results were easily tested by PCR-RFLP. This rapid and accurate screening system will be useful for detection of newborn infants with SMA.

Spinal Muscular Atrophy: New Screening System with Real-Time mCOP-PCR and PCR-RFLP for SMN1 Deletion

BACKGROUND

Spinal Muscular Atrophy (SMA) is a common autosomal recessive neuromuscular disorder characterized by degeneration or loss of lower motor neurons. More than 95% of SMA patients show homozygous deletion for the survival motor neuron 1 (SMN1) gene. For the screening of SMN1 deletion, it is necessary to differentiate SMN1 from its highly homologous gene, SMN2. We developed a modified competitive oligonucleotide priming-PCR (mCOP-PCR) method using dried blood spot (DBS)-DNA, in which SMN1 and SMN2-specific PCR products are detected with gel-electrophoresis. Next, we added a targeted pre-amplification step prior to the mCOP-PCR step, to avoid unexpected, non-specific amplification. The pre-amplification step enabled us to combine mCOP-PCR and real-time PCR. In this study, we combined real-time mCOP-PCR and PCR-restriction fragment length polymorphism (PCR-RFLP) to develop a new screening system for detection of SMN1 deletion.

METHODS

DBS samples of the subjects were stored at room temperature for a period of less than one year. Each subject had already been genotyped by the first PCR-RFLP using fresh blood DNA. SMN1/SMN2 exon 7 was collectively amplified using conventional PCR (targeted pre-amplification), the products of which were then used as a template in the real-time PCR with mCOP-primer sets. To confirm the results, the pre-amplified products were subject to the second PCR-RFLP.

RESULTS

The real-time mCOP-PCR separately amplified SMN1 and SMN2 exon7, and clearly demonstrated SMN1 deletion in an SMA patient. The results of the real-time mCOP-PCR using DBS-DNA were completely consistent with those of the first and second PCR-RFLP analysis.

CONCLUSION

In our new system for detection of SMN1 deletion, real-time mCOP-PCR rapidly proved the presence or absence of SMN1 and SMN2, and the results were easily tested by PCR-RFLP. This solid genotyping system will be useful for SMA screening.

Macrophage Migration Inhibitory Factor -173 G>C Gene Polymorphism Is Associated with Increased Risk of Nephrotic Syndrome in Children

INTRODUCTION

Nephrotic syndrome (NS), a common chronic pediatrickidney disease, is associated with immune system dysfunction.The exact role of MIF -137 G>C gene polymorphism on risk of NSis not clear. The current study aimed to evaluate the relationshipbetween MIF -173 G>C (rs755622) variant and susceptibility to NS.

METHODS

This case-control study conducted on 134 children withNS and 141 healthy children. Extraction of genomic DNA fromwhole blood was done using salting out method. Genotyping ofthe MIF -173 G>C polymorphism was performed using polymerasechain reaction restriction fragment length polymorphism (PCRRFLP)method.

RESULTS

The findings showed that MIF -173 G>C variant significantlyincreases the risk of NS in codominant (OR = 1.82, 95%CI = 1.08-3.08, P = 0.026, GC vs GG), dominant (OR = 1.90, 95%CI = 1.14-3.16,P = 0.015, GC+CC vs GG), overdominant (OR = 1.75, 95%CI = 1.04-2.94, P = 0.037, GC vs GG+CC) and allele (OR = 1.76, 95%CI = 1.13-2.74, P = 0.014, C vs G) inheritance models. Stratified analysisperformed by sex and response to treatment. The findings revealedthat this variant was associated with increased risk of NS in male.No correlation between the variant and response to treatment wasfound.

CONCLUSION

In summary, the results indicated that MIF -137 G>Cis significantly associated with increased risk of NS. More studieswith larger sample size among different ethnicities are needed toverify our findings.

The introduction of new hosts with human trade shapes the extant distribution of Toxoplasma gondii lineages

Toxoplasma gondii is a zoonotic protozoan with a worldwide occurrence, but the determinants of the current pattern in the geographical distribution of T. gondii lineages and strains remain poorly understood. To test the influence of human trade on T. gondii populations, we conducted a population genetic study of 72 T. gondii animal isolates from Senegal, a West African country in which the ongoing inland progress of invasive murine hosts (introduced in port cities of Senegal since the 16th century by European sailors) is well described. Isolates were mainly collected on free-range poultry, which are considered as relevant bioindicators of T. gondii strain diversity in the domestic environment. Sampling was conducted in two port cities of Senegal (Dakar and Saint-Louis) and in one inland region (Kedougou). Population genetic analyses using 15 microsatellite markers revealed different patterns between port cities where lineages non-virulent for mice (type II, type III, and Africa 4) were predominant, and Kedougou where the mouse-virulent Africa 1 lineage was the most common. By considering the current spatial pattern in the inland progress of invasive rodents in Senegal, our results suggest that the invasive house mouse Mus musculus domesticus counter-selects the Africa 1 lineage in the invaded areas. The comparison of the microsatellite alleles of type II strains from Senegal to type II strains from other areas in Africa and Western Europe, using discriminant analysis of principal components and Network analysis, point to a mainly Western European origin of the type II lineage in Senegal. Collectively, these findings suggest that human-mediated intercontinental migrations of murine hosts are important vectors of T. gondii strains. Differential susceptibility of endemic and introduced murine hosts to various T. gondii strains probably determines the persistence of these strains in the environment, and therefore their availability for human and animal infection.

Relationship of S/R warfarin ratio with CYP2C9 genotypes in Pakistani population

Warfarin is administered as a racemic preparation of R- and S-enantiomers. S-warfarin is more potent than R-warfarin, so changes in blood levels of S-warfarin affect the anticoagulant response. This study was carried out to determine the effect of CYP2C9*2 and CYP2C9*3 polymorphisms on S/R warfarin ratio. A single blood sample was collected 12-16 hours after drug administration from 170 stable patients fulfilling the criteria. Genotyping of the CYP2C9 polymorphisms was done by polymerase chain reaction-restriction fragment length polymorphism assay. S- and R-warfarin enantiomers extraction from plasma was accomplished by a validated HPLC method. The concentration of S-warfarin was significantly different among CYP2C9 genotypes (p =0.018) whereas there was no effect on R-warfarin (p =0.134). There was statistically significant effect of different CYP2C9 genotypes on S/R warfarin ratio (p=0.000). It is concluded that CYP2C9 polymorphisms influence CYP2C9 enzymatic activity in turn affecting S-warfari levels but not R-warfarin, thus leading to different S/R warfarin enantiomers ratio among different CYP2C9 genotypes.

Toll Like Receptor-4 Gene Polymorphism and Susceptibility to Pulmonary Tuberculosis

Tuberculosis (TB) affects human life globally for a long time. The difference in clinical outcome of infection suggests that host genetic makeup is responsible for such variability. Toll like receptors (TLRs) are pattern recognition receptors and have a significant role in mycobacterial recognition by the innate immune system. TLR-4 is the key receptor in initiation of innate immunity against M. tuberculosis. This study investigated whether variants in TLR-4 896A/G (Asp299Gly) and TLR-4 1196C/T (Thr399Ile) genes are related with susceptibility or resistance to pulmonary tuberculosis (PTB) in Saudi population. Genotyping of TLR-4 896A/G, TLR-4 1196C/T gene was performed by polymerase chain reaction followed by restriction fragment length polymorphism (PCR -RFLP) in 60 PTB patients and 60 control subjects. The A allele at (896A/G) was more frequent in the control group while G allele was more common in PTB patients. The frequency of T allele of (1196C/T) polymorphism was significantly increased in PTB patients as compared to the control group (P < 0.001; Odds ratio (OR) 2.79, 95% Confidence interval (CI) 1.65-4.72). A trend toward increased frequency of TT and CT genotypes of TLR4 at (1196C/T) were also observed in PTB patients as compared to control group (48.3% vs. 26, 7%, and 21.7% vs. 15%), respectively. This study suggests that that TLR4 polymorphism especially TLR4 rs4986791 may be associated with increase susceptibility to pulmonary tuberculosis, and C allele of rs4986791 is a promising protective factor for tuberculosis susceptibility in Saudi population.

Vitamin D receptor (VDR) TaqI polymorphism, vitamin D and bone mineral density in patients with inflammatory bowel diseases

BACKGROUND

A common feature in the etiology of inflammatory bowel disease (IBD) and osteoporosis is a complex genetic background. Moreover, it has been shown that some of the susceptibility loci overlap for both diseases. One of the genes that may be involved in the pathogenesis of IBD as well as decreased bone mass is the vitamin D receptor (VDR) gene.

OBJECTIVES

The aim of this study was to investigate the association of the TaqI polymorphism (rs731236, c.1056T >C) in the VDR gene with serum vitamin D concentration and bone mineral density (BMD) in patients with IBD.

MATERIAL AND METHODS

A total of 172 IBD patients (85 with Crohn's disease (CD) and 87 with ulcerative colitis (UC)) and 39 healthy controls were enrolled in the study. Polymorphism was determined with polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). Bone mineral density was measured at the lumbar spine (L2-L4) and the femoral neck (FN) using dual-energy x-ray absorptiometry (DEXA). Serum concentrations of 25-hydroxyvitamin D were determined using electrochemiluminescence binding assay (ECLIA).

RESULTS

Our studies revealed that serum vitamin D concentration in IBD patients was not lowered in comparison with healthy controls. Patients with CD presented more advanced osteopenia and osteoporosis. Individuals with UC carrying the TaqI tt genotype of VDR gene showed significantly higher FN BMD than carriers of TT and Tt genotypes (p = 0.02). Moreover, tt genotype was present with higher frequency in UC patients than in controls and CD patients (23% vs 7.7% and 16.5%, respectively).

CONCLUSIONS

The tt genotype may have a protective effect on BMD in UC patients.

Respiration induced by substrate and bacteria diversity after application of diuron, hexazinone, and sulfometuron-methyl alone and in mixture

After application, herbicides often reach the soil and affect non-target soil microorganisms, decreasing their population, diversity or affecting metabolic activity. Therefore, laboratory studies were performed to evaluate the effects of diuron, hexazinone and sulfometuron-methyl alone and mixed upon carbon transformation by soil microorganisms in clayey and sandy soils and the effect on bacterial diversity and structure. Control treatment without herbicide application was also performed. Sub-samples from the control and herbicide treatments (10 g - in triplicate) were collected before herbicide application and 7, 14, 28 and 42 days after treatment (DAT), then 1 mL of ¹⁴C-glucose solution was applied. The released ¹⁴CO₂ was trapped in 2 M NaOH solution and the radioactivity was analyzed by liquid scintillation counting (LSC), 12 h after glucose application. The effect of herbicides on bacterial diversity was evaluated by T-RFLP. The experiment was conducted in a complete randomized design. Hexazinone did not affect ¹⁴CO₂ evolution. Diuron showed a greater ¹⁴CO₂ evolution in sandy and clayey soil, while sulfometuron-methyl led to an increase in sandy soil, at 42 DAT. A greater evolution of carbon was observed in the treatment with herbicide mixture in sandy soil, compared with the same treatment in clayey soil or control. However, the herbicide mixture application did not affect the soil biological activity measured by the respiration rate induced by substrate. On the other hand, the herbicide mixtures affected the bacterial diversity in both soils, being the strongest effect to diuron and sulfometuron-methyl in clayey soil and hexazinone in sandy soil.

Antimicrobial resistances, and molecular typing of Campylobacter jejuni isolates, separated from food-producing animals and diarrhea patients in Iran

The aims of this study were to regain new epidemiology information about frequency, drug resistance rates, and typing of Campylobacter jejuni (C. jejuni) isolates, obtained from some poultry and cattle farms, slaughterhouses, and people with diarrhea. In this regard, Minimal Inhibitory Concentration (MIC) of several antibiotics and the associated antibiotic resistance genes, including tetO, tetA, cmeB, and bla_OXA-61 were evaluated. The isolates were also typed, using the Fla-RFLP method. Generally, between 233 food animal samples, 80 (34.33%) C. jejuni were isolated. Moreover, 20 out of 74 (27%) human specimens suspected to infectious diarrhea were C. jejuni positive. High frequencies of resistance to tetracycline (100%), ciprofloxacin (95%), and nalidixic acid (86%), and low frequencies of resistance to florfenicol (0%), erythromycin (5%), and gentamicin (8%) were observed. Furthermore, in the tetracycline-resistant isolates, the existences of tetO, tetA, and cmeB were 86%, 23%, and 48%, respectively. There was a significant correlation between the cluster types obtained from Fla-RFLP method and antibiotic resistance pattern. The results suggested that the genomic link between Campylobacter spp. should be always evaluated in each country to provide an insight about the Campylobacter spp., spread in the region, in order to implement the health-controlling programs efficiently.

Isolation and Genetic Characterization of Toxoplasma gondii from Tissues of Wild Turkeys (Meleagris gallopavo) in Pennsylvania

Toxoplasmosis in wild turkeys (Meleagris gallopavo) is of epidemiological interest because turkeys feed from the ground, and detection of infection in turkeys indicates contamination by oocysts in the environment. During the 2018 spring hunting season in Pennsylvania, fresh (unfixed, not frozen) samples were obtained from 20 harvested wild turkeys and tested for Toxoplasma gondii infection. Hearts from all wild turkeys and skeletal muscle from 1 were bioassayed for T. gondii by inoculation in outbred Swiss Webster (SW) and interferon-gamma gene knockout (KO) mice. Antibodies to T. gondii were detected in 1:5 dilution of neat serum from 5 of 15 wild turkeys and in fluid from the heart of 1 of 4 wild turkeys with the modified agglutination test (MAT); neat serum was not available from 4 wild turkeys. Viable T. gondii was isolated from hearts of 5 wild turkeys, 1 with MAT of 1:10, 1 with MAT of 1:5, and 3 seronegative (MAT < 1:5). Toxoplasma gondii was isolated from both heart and skeletal muscle in the 1 wild turkey that had skeletal muscle submitted. The KO mice inoculated with tissue from all 5 infected wild turkeys died or were euthanatized when ill, 7-21 days post-inoculation (PI). Tachyzoites were detected in lungs of all KO mice, and the T. gondii strains were successfully propagated in cell culture. The SW mice inoculated with tissues of wild turkeys remained asymptomatic, and tissue cysts were seen in the brains of infected mice when euthanatized in good health at 46 days PI; 1 of the 2 SW mice inoculated with the heart of 1 turkey died on day 26, and tachyzoites were detected in its lung. Genetic typing on DNA extracted from culture-derived tachyzoites using the PCR restriction fragment length polymorphism with 10 genetic markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico) revealed that 4 isolates belonged to ToxoDB PCR-RFLP genotype #5 and 1 was genotype #216.

Structural, physiological and genetic diversification of Silene vulgaris ecotypes from heavy metal-contaminated areas and their synchronous in vitro cultivation

Results provide significant comparison of leaf anatomy, pigment content, antioxidant response and phenolic profile between individuals from miscellaneous populations and describe unified cultivation protocols for further research on stress biology. The plant communities growing on heavy metal-polluted areas have attracted considerable attention due to their unique ability to tolerate enormous amounts of toxic ions. Three ecotypes of Silene vulgaris representing calamine (CAL), serpentine (SER) and non-metallicolous (NM) populations were evaluated to reveal specific adaptation traits to harsh environment. CAL leaves presented a distinct anatomical pattern compared to leaves of SER and NM plants, pointing to their xeromorphic adaptation. These differences were accompanied by divergent accumulation and composition of photosynthetic pigments as well as antioxidant enzyme activity. In CAL ecotype, the mechanism of reactive oxygen species scavenging is based on the joint action of superoxide dismutase and catalase, but in SER ecotype on superoxide dismutase and guaiacol-type peroxidase. On the contrary, the concentration of phenylpropanoids and flavonols in the ecotypes was unchanged, implying the existence of similar pathways of their synthesis/degradation functioning in CAL and SER populations. The tested specimens showed genetic variation (atpA/MspI marker). Based on diversification of S. vulgaris populations, we focused on the elaboration of similar in vitro conditions for synchronous cultivation of various ecotypes. The most balanced shoot culture growth was obtained on MS medium containing 0.1 mg l^-1 NAA and 0.25 mg l^-1 BA, while the most abundant callogenesis was observed on MS medium enriched with 0.5 mg l^-1 NAA and 5.0 mg l^-1 BA. For the first time, unified in vitro protocols were described for metallophytes providing the opportunity to conduct basic and applied research on stress biology and tolerance mechanisms under freely controlled conditions.

Molecular Survey for Pathogens and Markers of Permethrin Resistance in Human Head Lice (Phthiraptera: Pediculidae) from Madagascar

Human infestation with head lice, Pediculus humanus capitis De Geer, is the most prevalent ectoparasitic condition in the modern world. The purpose of this study was to test human head lice from Madagascar for infection with 2 louse-borne bacteria, Bartonella quintana and Acinetobacter spp. including Acinetobacter baumannii, to assess the potential risk of exposure to these pathogens in rural populations experiencing head-louse pediculosis. A second aim was to determine the occurrence of a biomarker for permethrin resistance in head lice from 6 isolated human communities in Madagascar. Deoxyribonucleic acid (DNA) of B. quintana was detected using species-specific Fab3 gene TaqMan in 12.6% of lice from 4 villages. DNA of Acinetobacter spp. was detected using rpoB TaqMan in 42.1% of lice collected from all locations; 58.3% of rpoB-positive lice had the bla_OXA51-like enzyme gene specific for A. baumannii. The kdr-resistant allele was detected in 70% of lice tested and was found in lice from each location. These results provide the first information regarding these combined characteristics of head-louse infestations in Madagascar. This approach can be applied to larger and broader surveys of lice from pediculosis capitis occurring in other geographic locations.

PCR-RFLP analyses of Leishmania species causing cutaneous and mucocutaneous leishmaniasis revealed distribution of genetically complex strains with hybrid and mito-nuclear discordance in Ecuador

PCR-Restriction Fragment Length Polymorphism (RFLP) analyses targeting multiple nuclear genes were established for the simple and practical identification of Leishmania species without using expensive equipment. This method was applied to 92 clinical samples collected at 33 sites in 14 provinces of Ecuador, which have been identified at the species level by the kinetoplast cytochrome b (cyt b) gene sequence analysis, and the results obtained by the two analyses were compared. Although most results corresponded between the two analyses, PCR-RFLP analyses revealed distribution of hybrid strains between Leishmania (Viannia) guyanensis and L. (V.) braziliensis and between L. (V.) guyanensis and L. (V.) panamensis, of which the latter was firstly identified in Ecuador. Moreover, unexpected parasite strains having the kinetoplast cyt b gene of L. (V.) braziliensis and nuclear genes of L. (V.) guyanensis, L. (V.) panamensis, or a hybrid between L. (V.) guyanensis and L. (V.) panamensis were identified. This is the first report of the distribution of a protozoan parasite having mismatches between kinetoplast and nuclear genes, known as mito-nuclear discordance. The result demonstrated that genetically complex Leishmania strains are present in Ecuador. Since genetic exchanges such as hybrid formation were suggested to cause higher pathogenicity in Leishmania and may be transmitted by more species of sand flies, further country-wide epidemiological studies on clinical symptoms, as well as transmissible vectors, will be necessary.

Leishmaniasis caused by intracellular protozoa of the genus Leishmania is a neglected tropical disease widely distributing worldwide, especially in tropical and subtropical areas. Approximately 20 species are known to be pathogenic to humans, of which eight species have been recorded as causative agents of cutaneous and mucocutaneous leishmaniases in Ecuador. Since infecting species are the major determinant of clinical outcomes, identification at the species level is important for the treatment and prognosis. The parasite species have been identified conventionally by multilocus enzyme electrophoresis (MLEE) and recently by genetic analysis such as sequencing and genotyping. In the present study, PCR-Restriction Fragment Length Polymorphism (RFLP) targeting multiple nuclear genes was employed, and the results were compared with those obtained by kinetoplast cytochrome b (cyt b) gene sequence analysis, which is widely applied to species identification. Although most results corresponded between the two analyses, PCR-RFLP revealed presence of unexpected genetically complex Leishmania strains having characteristics of hybrid and mito-nuclear discordance. Since hybrid strains of Leishmania were suggested to increase disease severity and may be transmitted by a wider range of sand fly species, careful epidemiological research, including clinical courses and vector research, will be needed.

Associations of TLR4 gene polymorphisms with the risk of age-related macular degeneration in a Chinese Han population

The study was designed to reveal the relationship of toll-like receptor 4 (TLR4, rs1927914 and rs1927907) polymorphisms with risk of age-related macular degeneration (AMD), as well as the adjustment of this association by some environmental and lifestyle factors in Chinese Han population.TLR4 polymorphisms were genotyped by polymerase chain reaction-restricted fragment length polymorphisms and direct sequencing method in 138 AMD patients and 146 healthy controls. Genotype distribution in the control group was checked with Hardy-Weinberg equilibrium. Association of TLR4 polymorphisms and AMD risk was evaluated by χ test and adjusted by age and sex, smoking and drinking. Odds ratio (OR) with 95% confidence interval (95% CI) was used to represent the association strength. Logistic regressive analysis was used to calculate the adjusted OR values.CC genotype of rs1927914 had significantly lower frequency in AMD patients (P = .010), indicated a negative association with AMD risk (crude: OR = 0.358, 95% CI = 0.162-0.791; adjusted: OR = 0.355, 95% CI = 0.160-0.789). C allele of rs1927914 might decrease the susceptibility of AMD (crude: OR = 0.698, 95% CI = 0.497-0.982; adjusted: OR = 0.698, 95% CI = 0.495-0.984). No significant association has been discovered between TLR4 rs1927907 polymorphism and AMD susceptibility. Strong linkage disequilibrium existed between rs1927914 and rs1927907 polymorphisms. C-C haplotype was negatively associated with AMD risk (OR = 0.242, 95% CI = 0.121-0.485; OR = 0.242, 95% CI = 0.120-0.488).CC genotype and C allele of rs1927914 were significantly associated with the decreased AMD susceptibility.

Fine mapping of Rha2 in barley reveals candidate genes for resistance against cereal cyst nematode

The cereal cyst nematode resistance locus Rha2 was mapped to a 978 kbp region on the long arm of barley chromosome 2H. Three candidate genes are discussed. The cereal cyst nematode (CCN) Heterodera avenae is a soil-borne obligate parasite that can cause severe damage to cereals. This research involved fine mapping of Rha2, a CCN resistance locus on chromosome 2H of barley. Rha2 was previously mapped relative to restriction fragment length polymorphisms (RFLPs) in two mapping populations. Anchoring of flanking RFLP clone sequences to the barley genome assembly defined an interval of 5077 kbp. Genotyping-by-sequencing of resistant and susceptible materials led to the discovery of potentially useful single nucleotide polymorphisms (SNPs). Assays were designed for these SNPs and applied to mapping populations. This narrowed the region of interest to 3966 kbp. Further fine mapping was pursued by crossing and backcrossing the resistant cultivar Sloop SA to its susceptible ancestor Sloop. Evaluation of F₂ progeny confirmed that the resistance segregates as a single dominant gene. Genotyping of 9003 BC₂F₂ progeny identified recombinants. Evaluation of recombinant BC₂F₃ progeny narrowed the region of interest to 978 kbp. Two of the SNPs within this region proved to be diagnostic of CCN resistance across a wide range of barley germplasm. Fluorescence-based and gel-based assays were developed for these SNPs for use in marker-assisted selection. Within the candidate region of the reference genome, there are nine high-confidence predicted genes. Three of these, one that encodes RAR1 (a cysteine- and histidine-rich domain-containing protein), one that is predicted to encode an acetylglutamate kinase and one that is predicted to encode a tonoplast intrinsic protein, are discussed as candidate genes for CCN resistance.

Association of Interleukin-31 gene polymorphisms with risk of cryptorchidism in a Chinese population

This study aims to investigate the possible association between Interleukin-31 (IL-31) gene polymorphisms and cryptorchidism risk.Two single nucleotide polymorphisms of IL-31, rs7977932 (C/G) and rs4758680 (C/A), were selected to be investigated in this study. Polymerase chain reaction-restriction fragment length polymorphism methods were used to discriminate the selected single nucleotide polymorphisms of IL-31 gene. A hospital-based case-control study of 112 cryptorchidism patients and 425 healthy controls was conducted.The frequencies of the C allele of rs4758680 in the patients with cryptorchidism were significantly higher compared with those in controls (89% vs 83%, P = .02, OR = 0.58, 95% CI = 0. 37-0.92). Compared with CC genotype in dominant model, notable decreased frequencies of A carriers (CA/AA genotypes) were observed in cryptorchidism patients (P = . 03, OR = 0.58, 95% CI = 0.35-0.96).Results demonstrated that IL-31 gene polymorphisms were associated with the genetic susceptibility to cryptorchidism in a Chinese population. Compared with CC genotype, the A carriers (CA/AA genotypes) of rs4758680 were protect factors in cryptorchidism susceptibility.

KLHL3 single-nucleotide polymorphism is associated with essential hypertension in Chinese Han population

Hypertension, including secondary and essential hypertension (EH) variants, is a multifactorial disease, affecting more than one billion people worldwide. Secondary hypertension results from mutations in the putative gene KLHL3 (Kelch-like protein 3); however, it has not been reported whether the KLHL3 gene polymorphisms are associated with EH. Here, we investigated the association between KLHL3 (rs2301708 and rs7444370) polymorphisms and EH in the Chinese Han population.This case-control study included 522 subjects-260 patients with EH and 262 normotensive controls matched for age, gender, body mass index (BMI), hemoglobin A1c (HbA1c), total cholesterol (TC), triglyceride (TG), and levels of Na, K, and Cl. The distribution of functional rs2301708 and rs7444370 polymorphisms within the KLHL3 gene was assessed through polymerase chain reaction (PCR) and restriction-fragment length polymorphism (RFLP).There was no significant difference in allelic and genotypic frequencies of KLHL3 rs2301708 between the EH and normotensive groups; however, the rs7444370 T allele and CT genotype in females was significantly associated with a protective effect against EH (P = .001, P = .002; P = .019, P = .052), and the haplotype CT of rs2301708 and rs7444370 among females in the EH group was less than in the normotensive group (P = .000; P = .007).The KLHL3 rs7444370 variant could be a protective factor in the pathogenesis of females' EH.

Phylogeny and distribution of Bradyrhizobium symbionts nodulating cowpea (Vigna unguiculata L. Walp) and their association with the physicochemical properties of acidic African soils

In the N2-fixing symbiosis, the choice of a symbiotic partner is largely influenced by the host plant, the rhizobial symbiont, as well as soil factors. Understanding the soil environment conducive for the survival and multiplication of root-nodule bacteria is critical for microbial ecology. In this study, we collected cowpea-nodules from acidic soils in Ghana and South Africa, and nodule DNA isolates were characterized using 16S-23S rRNA-RFLP, phylogenetic analysis of housekeeping and symbiotic genes, and bradyrhizobial community structure through canonical correspondence analysis (CCA). The CCA ordination plot results showed that arrow of soil pH was overlapping on CCA2 axis and was the most important to the ordination. The test nodule DNA isolates from Ghana were positively influenced by soil Zn, Na and K while nodule DNA isolates from South Africa were influenced by P. The amplified 16S-23S rRNA region yielded single polymorphic bands of varying lengths (573-1298bp) that were grouped into 28 ITS types. The constructed ITS-dendrogram placed all the nodule DNA isolates in five major clusters at low cut-off of approx. 0.1 Jaccard's similarity coefficient. The phylogenetic analysis of 16S rRNA and housekeeping genes (glnII, gyrB, and atpD) formed distinct Bradyrhizobium groups in the phylogenetic trees. It revealed the presence of highly diverse bradyrhizobia (i.e. Bradyrhizobium vignae, Bradyrhizobium elkanii, Bradyrhizobium iriomotense, Bradyrhizobium pachyrhizi, and Bradyrhizobium yuanmingense) together with novel/unidentified bradyrhizobia in the acidic soils from Ghana and South Africa. Discrepancies noted in the phylogenies of some nodule DNA isolates could be attributed to horizontal gene transfer or recombination.

Leishmania (Viannia) braziliensis type 2 as probable etiological agent of canine cutaneous leishmaniasis in Brazilian Amazon

Canine cutaneous leishmaniasis (CCL) is a zoonosis of public health interest, and in the Americas, Leishmania (Viannia) braziliensis has been identified as the main etiological agent. The present study sought to investigate Leishmania spp. infection in domestic dogs from a rural area of the Xapuri municipality, Acre state, Brazilian Amazonia. For this purpose, visits were carried out to domiciles where the human cases of American cutaneous leishmaniasis (ACL) occurred, followed by the clinical evaluation of the animals in search of clinical signs suggestive of CCL. Blood samples were collected from 40 dogs, 13 of which had lesions suggestive of CCL, and biopsies of these lesions were performed. The methods used were Neal, Novy, and Nicolle’s (NNN) medium cultures and direct parasitological examination. Further, to detect and characterize Leishmania DNA some molecular techniques were performed such as conventional polymerase chain reaction (PCR) and sequencing targeting SSU rDNA and ITS1, restriction fragment length polymorphism (RFLP) and high resolution melting (HRM) analysis targeting hsp70. The investigation revealed that the results obtained from the parasitological methods were negative. In PCR by ITS1 and network topology sequences, six strains from dogs, isolated from the Peruvian Andes, appeared identical to Leishmania (Viannia) braziliensis type 2 (99–100%). By other molecular methods these samples turned out to be positive to Leishmania (Viannia) sp.. The diagnosis of Leishmania in domestic dogs from Acre state showed a high proportion of infected animals, and the occurrence of L. braziliensis type 2 in Brazil for the first time. This new report suggests that L. braziliensis type 2 is both trans- and cis-Andean. However, more studies are needed regarding the clinical and diagnostic aspects of this species of Leishmania.