The methylome of buccal epithelial cells is influenced by age, sex, and physiological properties.

Epigenetic modifications, particularly DNA methylation, have emerged as regulators of gene expression and are implicated in various biological processes and disease states. Understanding the factors influencing the epigenome is essential for unraveling its complexity. In this study, we aimed to identify how the methylome of buccal epithelial cells, a noninvasive and easily accessible tissue, is associated with demographic and health-related variables commonly used in clinical settings, such as age, sex, blood immune composition, hemoglobin levels, and others. We developed a model to assess the association of multiple factors with the human methylome and identify the genomic loci significantly impacted by each trait. We demonstrated that DNA methylation variation is accurately modeled by several factors. We confirmed the well-known impact of age and sex and unveiled novel clinical factors associated with DNA methylation, such as blood neutrophils, hemoglobin, red blood cell distribution width, high-density lipoprotein cholesterol, and urea. Genomic regions significantly associated with these traits were enriched in relevant transcription factors, drugs, and diseases. Among our findings, we showed that neutrophil-impacted loci were involved in neutrophil functionality and maturation. Similarly, hemoglobin-influenced sites were associated with several diseases, including aplastic anemia, and the genomic loci affected by urea were related to congenital anomalies of the kidney and urinary tract. Our findings contribute to a better understanding of the human methylome plasticity and provide insights into novel factors shaping DNA methylation patterns, highlighting their potential clinical implications as biomarkers and the importance of considering these physiological traits in future medical epigenomic investigations.NEW & NOTEWORTHY We have developed a quantitative model to assess how the human methylome is associated with several factors and to identify the genomic loci significantly impacted by each trait. We reported novel health-related factors driving DNA methylation patterns and new site-specific regulations that further elucidate methylome dynamics. Our study contributes to a better understanding of the plasticity of the human methylome and unveils novel physiological traits with a potential role in future medical epigenomic investigations.

Metabarcoding of colonic cleansing fluid reveals unique bacterial members of mucosal microbiota associated with Inflammatory Bowel Disease.

BACKGROUND: Inflammatory Bowel Disease (IBD) is a group of chronic idiopathic inflammatory diseases of the gastrointestinal (GI) tract associated with the dysbiosis of gut microbiota. Metabarcoding-based profiling of the gut microbiota of IBD patients is generally based on the stool samples collected from individual patients which rarely represent the mucosa-associated microbiota. The ideal sampling strategy for routine monitoring of the mucosal component of IBD has yet to be determined. METHODS: We hereby compare the microbiota composition of the colonic cleansing fluid (CCF) collected during colonoscopy with stool samples from IBD patients. The relationship between IBD and gut microbiota was revealed through the application of the 16S rRNA amplicon sequencing-based metabarcoding approach. CCF and stool samples were collected from IBD patients with Crohn's disease and ulcerative colitis. RESULTS: The present study shows significant differences in the microbial composition of CCF samples, presumably indicating changes in the mucosal microbiota of IBD patients as compared to the control group. Short-chain fatty acid-producing bacteria under the family Lachnospiraceae, the actinobacterial genus Bifidobacterium, the proteobacterial Sutterella and Raoultella are found to contribute to the microbial dysbiosis of the mucosal flora in IBD patients. CONCLUSIONS: CCF microbiota has the capacity to distinguish IBD patients from healthy controls and, thus, may constitute an alternative analysis strategy for the early diagnosis and disease progression in IBD biomarker research.

Galectin-3 as a Potential Prognostic Biomarker for COVID-19 Disease: A Case-Control Study.

Background Recent studies have investigated the importance of Galetin-3 in inflammation, fibrosis, cell proliferation, cardiac disease, diabetes, and tumor formation. Aims This study aims to investigate the role of the Galectin-3 level in the diagnosis of COVID-19 pneumonia and the value of the Galectin-3 level in predicting the clinical course of the patient. Methods This study employed a prospective, case-control study design and was conducted at Bakircay University Cigli Training and Research Hospital. A total of 100 patients (40 had moderate and 60 had severe/critical COVID-19 disease according to World Health Organisation guidelines) and 50 non-symptomatic healthy volunteers participated in the study. Blood samples were taken from patients at the time of hospital admission, after which serum was isolated. Following the isolation of serum, Galectin-3 levels were evaluated using the enzyme-linked immunosorbent assay (ELISA) method.  Results The serum Galectin-3 level was measured as 13.57 (10.9-16.4) ng/mL in the control group, 13.52 (10.69-16.6) ng/mL in the moderate disease group, and 11.65 (6.09-14.33) ng/mL in the severe/critical disease group. Serum Galectin-3 levels were significantly lower in the severe/critical disease group compared to the control and moderate disease groups (p=0.001 and p=0.019, respectively). Using ROC analysis, a larger area under the curve (AUC) for the serum Galectin-3 levels of the control group (AUC=0.622, 95% CI =0.529-0.714; p=0.015) was calculated compared to the COVID-19 patient group for the diagnosis of COVID-19 disease. The Galectin-3 level was found to be 75% sensitive and 50% specific at a cut-off level of 11.3 ng/mL in predicting the need for ICU treatment. Conclusion Galectin-3 levels may be a beneficial biomarker in predicting the clinical severity of COVID-19 disease when used in conjunction with other known biomarkers, at the time of admission to the emergency department (ED).

Investigation of Dientamoeba fragilis and Blastocystis in patients from Turkey with ulcerative colitis and irritable bowel syndrome: Any relation with genotypes?

Blastocystis sp. and Dientamoeba fragilis are two most common protists worldwide, whose pathogenic potentials are a matter of debate since their discovery. This study aims to investigate the relationship between the activation of ulcerative colitis (UC) and irritable bowel syndrome (IBS) with these protists. A total of 100 patients (35 IBS, 35 active UC, and 30 remittent UC), diagnosed at Hacettepe University Adult Hospital (Ankara, Turkey), were screened for D. fragilis and Blastocystis sp. with microscopic examination using the methods of wet mount, trichrome staining, conventional PCR, nested PCR, real-time PCR and genotyping. Eight patients (4 IBS, 2 active, and 2 remittent UC patients) were found to be D. fragilis positive. 18S rRNA region of the parasite was amplified in four of the patients, whereas cathepsin L-like cysteine peptidase; clan Sc, family S9, serine peptidase; and clan MH, family M20 metallopeptidase in six different patients. All isolates were Genotype 1. Sequence results showed very limited diversity. A total of nine patients (3 IBS, 5 active UC, 1 remittent UC) were found to be positive for Blastocystis sp., all of which were Subtype 3. One active UC and one IBS patient were found to be positive for both parasites. No statistically significant difference was detected between the patient groups in means of parasite detection. D. fragilis was found to be related to older age (p=0,045). In our study, no significant correlation was identified between D. fragilis and Blastocystis sp., and the activation of UC and IBS. More studies are needed on the host-parasite relationship, including the role of gut microbiota, together with transcriptomic and metabolomic assessments to unveil the pathogenicity of both protists.

Characterisation of the Leishmania donovani/L. infantum Hybrid Isolated from an Autochothonous Kala-Azar Patient: Preliminary Results of an In Vivo Model

Objective: In the present study, preliminary outcomes of the in vivo assessment of a Leishmania donovani/L. infantum hybrid isolated from a hospitalised patient with visceral leishmaniasis in Manisa and identified through analysis of the Leishmania-specific ITS-1, hsp70 and cpb gene regions are presented in comparison with reference strains of L. donovani and L. infantum. Methods: Three different study groups [(SG); n=16 mice each] and a control group (n=8 mice) were established with female Balb/C mice weighing 25-30 g. Reference L. donovani (MHOM/IN/1980/DD8), reference L. infantum (MHOM/TN/1980/IP1) and a L. donovani/L. infantum hybrid (MHOM/TR/2014/CBVL-LI/ LD), stored in liquid nitrogen, were thawed, cultured and incubated at 25 °C. A 15-µL dose of 1x108/mL promastigotes of three strains was applied to the tail veins of mice in the SG. After the mice were sacrificed, the liver and spleen tissues were removed and stored for immunological, immunohistochemical and pathological analyses. Results: The presence of infection in the liver and spleen tissues of mice was detected both by a specific enzyme-linked immunosorbent assay test and from the recovery of Leishmania promastigotes from liver and spleen tissues in NNN medium. However, Leishmania amastigotes were not observed in the touch biopsy smears of livers or spleens in either of the SGs. In addition, no evidence of tissue damage was identified in the SGs after immunohistochemical staining (with antibodies against IL-9, CD-117, MBP, CD163, CD4, CD8 and CD31). Conclusion: The obtained results show that hybrid Leishmania and reference L. donovani and L. infantum strains reached the liver and spleens of Balb/C mice in SGs but were of no pathological consequence. Yet, these three Leishmania isolates caused skin lesions when applied subcutaneously in Balb/C mice in another study. The findings presented in this study will be reassessed upon completion of the project, once the final results are obtained.

Toxoplasmosis in Transplant Recipients, Europe, 2010-2014.

Transplantation activity is increasing, leading to a growing number of patients at risk for toxoplasmosis. We reviewed toxoplasmosis prevention practices, prevalence, and outcomes for hematopoietic stem cell transplant (HSCT) and solid organ transplant (SOT; heart, kidney, or liver) patients in Europe. We collected electronic data on the transplant population and prevention guidelines/regulations and clinical data on toxoplasmosis cases diagnosed during 2010-2014. Serologic pretransplant screening of allo-hematopoietic stem cell donors was performed in 80% of countries, screening of organ donors in 100%. SOT recipients were systematically screened in 6 countries. Targeted anti-Toxoplasma chemoprophylaxis was heterogeneous. A total of 87 toxoplasmosis cases were recorded (58 allo-HSCTs, 29 SOTs). The 6-month survival rate was lower among Toxoplasma-seropositive recipients and among allo-hematopoietic stem cell and liver recipients. Chemoprophylaxis improved outcomes for SOT recipients. Toxoplasmosis remains associated with high mortality rates among transplant recipients. Guidelines are urgently needed to standardize prophylactic regimens and optimize patient management.

[Amoebic liver abscess in a patient initially diagnosed with pneumonia: case report and discussion of relevant literature]. / Pnömoni Ön Tanili Bir Hastada Amebik Karaciger Absesi: Olgu Sunumu ve Ilgili Literatürün Degerlendirilmesi.

In one-third of the patients with amoebiasis, amoebic liver abscess (ALA) may occur after the penetration of amoebic trophozoites through the intestinal wall. ALA is seen mostly among men aged 20-45 years with a serious clinical outcome, with fever and abdominal pain on the right upper quadrant. Most patients have no recent history of amoebic colitis; indeed, they have neither gastrointestinal complaints nor Entamoeba histolytica (E. histolytica) cysts/trophozoites in their stools. Therefore, ultrasonography and serology are primary in ALA diagnosis, while searching for E. histolytica DNA in abscess fluid using PCR has been preferred as an effective and reliable method, lately. Early antimicrobial therapy is effective; however, for cases irresponsive to therapy after 72 hours and with large abscess, drainage or surgical intervention is indicated. If left untreated, ALA may disseminate to other organs and cause death. The data concerning the extra-intestinal manifestations of amebiasis in Turkey are limited. Here, a rare case of a young man with an initial diagnosis of pneumonia followed by the identification of ALA after radiological interventions and laboratory tests is presented and the relevant literature is discussed.

Effectiveness of peptone-yeast extract (P-Y) medium in the cultivation and isolation of Entamoeba histolytica/Entamoeba dispar in Turkish patients.

Amebiasis is a common protozoan infection worldwide, causing serious health problems in both children and adults. Today, almost 10% of the world population is infected with Entamoeba histolytica/Entamoeba dispar. The aims of this study were both the comparison of the reproduction rates and densities of E. histolytica/E. dispar in Robinson, Dobell-Laidlaw and P-Y culture media and isolation of E. histolytica/E. dispar from stool samples in Peptone-Yeast (P-Y) medium. Trophozoites and cysts of E. histolytica/E. dispar, maintained in Robinson medium, and stool samples of patients with amebiasis were inoculated into P-Y, Robinson and Dobell-Laidlaw culture media. Reproduction rates reached their peak levels 48 h after the inoculation in all culture media. Reproduction rates in P-Y and Robinson media were found similar; however, they were higher than the reproduction rate in Dobell-Laidlaw medium (p < 0.01); there was no statistically significant difference between the reproduction rates of P-Y and Robinson media (p > 0.05). Twelve isolates from 12 patients were cultivated in P-Y medium and checked for reproduction everyday for 7 days. Twelve of the 12 (100%) isolates were cultivated in P-Y medium, indicating that the P-Y was an effective medium for the isolation of E. histolytica/E. dispar in stool samples. According to these results, P-Y medium could be preferred in immunologic, serologic and molecular studies and, thus the definitive diagnosis of amebiasis due to its low cost and simple formula.

Serological levels of zinc, copper and iron elements among Giardia lamblia infected children in Turkey.

BACKGROUND: Giardiasis, an intestinal protozoan infection caused by Giardia lamblia, is common in Turkey, especially among children aged between 2- and 14-years-old. Effects of giardiasis on serological levels of zinc, copper and iron elements were assessed in this study. METHODS: A total of 45 children, aged between 2- and 14-years-old, who were admitted to the Pediatrics Department of Celal Bayar University Medical School with gastrointestinal complaints and diagnosed as having giardiasis by stool examinations in the Parasitology Department, were enrolled as the study group (SG). The control group (CG) consisted of 45 age-matched healthy children. Serological levels of zinc, copper and iron were measured by atomic absorption spectrophotometer in all samples. RESULTS: As a result of the study, serum zinc levels were 67.43 +/- 17.72 microg/dL and 145.20 +/- 9.13 microg/dL, copper levels were 198.45 +/- 39.14 microg/dL and 150 +/- 21.14 microg/dL and iron levels were 87.98 +/- 18.31 microg/dL and 160.45 +/- 45.40 microg/dL, in SG and CG, respectively. When compared separately as SG and CG, there was a statistically significant difference between the serological levels of all these elements. CONCLUSION: These results revealed that giardiasis increased the serological levels of copper, like other infectious agents. However, zinc and iron levels decreased during giardiasis due to malabsorption.

Giardiasis treatment in Turkish children with a single dose of ornidazole.

This study was designed to compare the treatment efficacy of single dose of ornidazole with 5 d treatments of ornidazole and metronidazole in children with giardiasis. 175 children, between 2 and 15 y old, whose stool samples were found to be positive for Giardia lamblia cysts and/or trophozoites by either saline-Lugol, formalin-ethyl acetate or trichrome staining, were enrolled in the study. Of these children, 105 were treated with a single dose of ornidazole: 35 with 30 mg/kg, 35 with 25 mg/kg and 35 with 20 mg/kg; 35 were treated with 25 mg/kg per day of ornidazole for 5 d in 2 doses and 35 children were treated with 20 mg/kg per day metronidazole for 7 d in 3 doses. All cases were examined on the 7th, 10th and 14th days after treatment by the same methods; clinical symptoms were also evaluated. Giardia lamblia was eradicated in 34 of 35 (97%), 34 of 35 (97%) and 33 of 35 (94%) patients treated with 30, 25 and 20 mg/kg single doses of ornidazole, respectively. Eradication was achieved in all 35 patients treated with 25 mg/kg per day ornidazole for 5 d and in 31 of 35 (89%) patients treated with metronidazole. There was no statistically significant difference among doses of ornidazole (p > 0.05); however, all ornidazole treatment regimens were significantly more effective than metronidazole treatment (p < 0.05). No important side-effects were detected in any patients and clinical symptoms disappeared in all. Single-dose ornidazole treatment could be considered as a proper and effective alternative method for the treatment of giardiasis in children.