Prokaryotic communities in the thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan salterns (Turkey) assessed by 16s rRNA amplicon sequencing

Prokaryotic communities and physico-chemical characteristics of 30 brine samples from the thalassohaline Tuz Lake (Salt Lake), Deep Zone, Kayacik, Kaldirim, and Yavsan salterns (Turkey) were analyzed using 16S rRNA amplicon sequencing and standard methods, respectively. Archaea (98.41% of reads) was found to dominate in these habitats in contrast to the domain Bacteria (1.38% of reads). Representatives of the phylum Euryarchaeota were detected as the most predominant, while 59.48% and 1.32% of reads, respectively, were assigned to 18 archaeal genera, 19 bacterial genera, 10 archaeal genera, and one bacterial genus that were determined to be present, with more than 1% sequences in the samples. They were the archaeal genera Haloquadratum, Haloarcula, Halorhabdus, Natronomonas, Halosimplex, Halomicrobium, Halorubrum, Halonotius, Halolamina, Halobacterium, and Salinibacter within the domain Bacteria. The genera Haloquadratum and Halorhabdus were found in all sampling sites. While Haloquadratum, Haloarcula, and Halorhabdus were the most abundant genera, two uncultured Tuz Lake Halobacteria (TLHs) 1 and 2 were detected in high abundance, and an additional uncultured haloarchaeal TLH-3 was found as a minor abundant uncultured taxon. Their future isolation in pure culture would permit us to expand our knowledge on hyper-saline thalassohaline habitats, as well as their ecological role and biomedical and biotechnological potential applications.The authors would like to express their gratitude to Marmara University Scientific Research Projects Commission (BAPKO) for funding

Heterogeneity of pollen food allergy syndrome in seven Southern European countries: The @IT.2020 multicenter study

Background Pollen food allergy syndrome (PFAS) is a frequently underdiagnosed disease due to diverse triggers, clinical presentations, and test results. This is especially relevant in geographic areas with a broad spectrum of pollen sensitization, such as Southern Europe. Objectives To elucidate similarities and differences of PFAS in nine Southern European centers and identify associated characteristics and unique markers of PFAS. Methods As part of the @IT.2020 Multicenter Study, 815 patients with seasonal allergic rhinitis (SAR), aged 10-60 years, were recruited in seven countries. They completed questionnaires regarding SAR, comorbidities, family history, and PFAS, and underwent skin prick testing (SPT) and serum IgE testing. Results Of the 815 patients, 167 (20.5%) reported PFAS reactions. Most commonly, eliciting foods were kiwi (58, 34.7%), peach (43, 25.7%), and melon (26, 15.6%). Reported reactions were mostly local (216/319, 67.7%), occurring within 5 min of contact with elicitors (209/319, 65.5%). Associated characteristics included positive IgE to at least one panallergen (profilin, PR-10, or nsLTP) (p = 0.007), maternal PFAS (OR: 3.716, p = 0.026), and asthma (OR: 1.752, p = 0.073). Between centers, heterogeneity in prevalence (Marseille: 7.5% vs. Rome: 41.4%, p < 0.001) and of clinical characteristics was apparent. Cypress played a limited role, with only 1/22 SPT mono-sensitized patients reporting a food reaction (p < 0.073). Conclusions PFAS is a frequent comorbidity in Southern European SAR patients. Significant heterogeneity of clinical characteristics in PFAS patients among the centers was observed and may be related to the different pollen sensitization patterns in each geographic area. IgE to panallergen(s), maternal PFAS, and asthma could be PFAS-associated characteristics

Heterogeneity of pollen food allergy syndrome in seven Southern European countries: The @IT.2020 multicenter study

Background Pollen food allergy syndrome (PFAS) is a frequently underdiagnosed disease due to diverse triggers, clinical presentations, and test results. This is especially relevant in geographic areas with a broad spectrum of pollen sensitization, such as Southern Europe. Objectives To elucidate similarities and differences of PFAS in nine Southern European centers and identify associated characteristics and unique markers of PFAS. Methods As part of the @IT.2020 Multicenter Study, 815 patients with seasonal allergic rhinitis (SAR), aged 10-60 years, were recruited in seven countries. They completed questionnaires regarding SAR, comorbidities, family history, and PFAS, and underwent skin prick testing (SPT) and serum IgE testing. Results Of the 815 patients, 167 (20.5%) reported PFAS reactions. Most commonly, eliciting foods were kiwi (58, 34.7%), peach (43, 25.7%), and melon (26, 15.6%). Reported reactions were mostly local (216/319, 67.7%), occurring within 5 min of contact with elicitors (209/319, 65.5%). Associated characteristics included positive IgE to at least one panallergen (profilin, PR-10, or nsLTP) (p = 0.007), maternal PFAS (OR: 3.716, p = 0.026), and asthma (OR: 1.752, p = 0.073). Between centers, heterogeneity in prevalence (Marseille: 7.5% vs. Rome: 41.4%, p &lt; 0.001) and of clinical characteristics was apparent. Cypress played a limited role, with only 1/22 SPT mono-sensitized patients reporting a food reaction (p &lt; 0.073). Conclusions PFAS is a frequent comorbidity in Southern European SAR patients. Significant heterogeneity of clinical characteristics in PFAS patients among the centers was observed and may be related to the different pollen sensitization patterns in each geographic area. IgE to panallergen(s), maternal PFAS, and asthma could be PFAS-associated characteristics

“Whole” vs. “fragmented” approach to EAACI pollen season definitions: A multicenter study in six Southern European cities

Background: The adequate definition of pollen seasons is essential to facilitate a correct diagnosis, treatment choice, and outcome assessment in patients with seasonal allergic rhinitis. A position paper by the European Academy of Allergy and Clinical Immunology (EAACI) proposed season definitions for Northern and Middle Europe. Objective: To test the pollen season definitions proposed by EAACI in six Mediterranean cities for seven pollen taxa. Methods: As part of the @IT.2020 multi-center study, pollen counts for Poaceae, Oleaceae, Fagales, Cupressaceae, Urticaceae (Parietaria spp.), and Compositae (Ambrosia spp., Artemisia spp.) were collected from January 1 to December 31, 2018. Based on these data, pollen seasons were identified according to EAACI criteria. A unified monitoring period for patients in AIT trials was created and assessed for feasibility. Results: The analysis revealed a great heterogeneity between the different locations in terms of pattern and length of the examined pollen seasons. Further, we found a fragmentation of pollen seasons in several segments (max. 8) separated by periods of low pollen counts (intercurrent periods). Potential monitoring periods included often many recording days with low pollen exposure (max. 341 days). Conclusion: The Mediterranean climate leads to challenging pollen exposure times. Monitoring periods for AIT trials based on existing definitions may include many intermittent days with low pollen concentrations. Therefore, it is necessary to find an adapted pollen season definition as individual solution for each pollen and geographical area

Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals

Copy number variants (CNV) are established risk factors for neurodevelopmental disorders with seizures or epilepsy. With the hypothesis that seizure disorders share genetic risk factors, we pooled CNV data from 10,590 individuals with seizure disorders, 16,109 individuals with clinically validated epilepsy, and 492,324 population controls and identified 25 genome-wide significant loci, 22 of which are novel for seizure disorders, such as deletions at 1p36.33, 1q44, 2p21-p16.3, 3q29, 8p23.3-p23.2, 9p24.3, 10q26.3, 15q11.2, 15q12-q13.1, 16p12.2, 17q21.31, duplications at 2q13, 9q34.3, 16p13.3, 17q12, 19p13.3, 20q13.33, and reciprocal CNVs at 16p11.2, and 22q11.21. Using genetic data from additional 248,751 individuals with 23 neuropsychiatric phenotypes, we explored the pleiotropy of these 25 loci. Finally, in a subset of individuals with epilepsy and detailed clinical data available, we performed phenome-wide association analyses between individual CNVs and clinical annotations categorized through the Human Phenotype Ontology (HPO). For six CNVs, we identified 19 significant associations with specific HPO terms and generated, for all CNVs, phenotype signatures across 17 clinical categories relevant for epileptologists. This is the most comprehensive investigation of CNVs in epilepsy and related seizure disorders, with potential implications for clinical practice

Context-Aware Engineering of Prokaryotic Chassis

As a unique multidisciplinary approach to the biological world, synthetic biology necessitates the work of a ‘designer’ to utilize existing paradigms of biology and engineer systems that successfully execute the desired biological and chemical functions. For these efforts, prokaryotic cells have long provided the necessary cellular machinery and biochemical substrates for the expression of synthetic products. This dependence on the genetic and chemical background of the prokaryotic host cell has been implicated to affect the cells’ viability and, conversely, the performance of the genetic circuit. The highly dynamic and complex environment of the cell poses a challenge for elucidating in real-time the type and breadth of unintended interactions which may occur in the engineered cell, namely orthogonality. In this thesis work, I present a systematic overview of how synthetic biologists have been addressing this challenge of measuring circuit-host orthogonality and delineate the implementation and testing of one of those methods for creating biosensors that incorporate endogenous Escherichia coli (E. coli) promoters to assess orthogonality. At large, this thesis work will highlight the importance of orthogonality as an irreplaceable benchmarking attribute of synthetic systems for engineering prokaryotic host cells in a context-aware manner

Karbapeneme Dirençli Acinetobacter baumannii Enfeksiyonlarının Tedavisinde Kullanılan Çeşitli Antibiyotik Kombinasyonları ve İn Vitro Sinerji Test Sonuçları (2002-2016)

Carbapenem resistant Acinetobacter baumannii is a bacterium that causes various hospital acquired infections, primarily ventilator-associated pneumonia and bloodstream infections. The multidrug resistance problem of the bacteria all over the world, is also a problem in our center. As the treatment options are decreasing combination therapies become a current issue. It is believed that in vitro synergy tests may guide to the selection of antibiotic combinations. The aim of this study was to present the antibiotic combinations used in the treatment of carbapenem resistant A.baumannii infections and the synergy test results of these combinations. A total of 71 carbapenem-resistant A.baumannii isolates from various clinical samples of patients in Hacettepe University Adult and Oncology Hospitals was included in the study. All isolates were from nosocomial infections that were being requested for synergy testing by the consulting physicians in the Department of Infectious Diseases and Clinical Microbiology between January 2002 and December 2016. Only one isolate from one patient was included in the analysis. The synergy test for these isolates was performed by E-test method. Of the total, 41 (58%) isolates were from various clinical samples of patients in intensive care units and 30 (42%) were from patients in different wards. Twenty-three of the isolates were obtained from bronchoalveolar lavage (BAL) fluid, 18 from pus, 14 from deep tracheal aspirate, 6 from central venous catheter, 5 from blood and 5 from other various samples. The fractional inhibition concentration (FIC) index for each combination was calculated and the results were interpreted as synergistic, additive, indifferent and antagonist. A total of 38 different combinations of antibiotics were tested. According to the frequency of synergistic activity, the combinations were; meropenem-colistin (11/12), meropenem-amikacin (7/9), meropenem-tobramycin (9/13), rifampicin-colistin (7/11), cefaperazone-sulbactam-tobramycin (8/16) and sefaperazon-sulbactam-amikacin (5/10). The most common antagonistic combinations were tigecyclin-colistin (2/6), meropenem-tobramycin (3/13), cefepim-tobramycin (4/19), rifampicin-colistin (2/11) combinations. In our center, different combinations of antibiotics are being used for the treatment of carbapenem-resistant A.baumannii due to the changing and increasing antibiotic resistance of the bacteria over the years. Sensitivity tests as well as synergy tests are used when selecting different combinations of antibiotics. However generalizability of the synergistic effect of combinations is limited. It is important to repeat these studies at regular intervals. In addition there is also a need for further studies to evaluate the correlation between in vitro laboratory results and in vivo clinical compliance.WoSScopu

Bilateral acute depigmentation of iris: 3-year follow-up of a case

Bilateral acute depigmentation of the iris (BADI) usually affecting young women, is a newly defined clinical diagnosis with bilateral symmetrical pigment loss of iris stroma without iris transillumination defect. Herein, we want to share the results of a 3-year-long follow-up of a 23-year old female patient with BADI. She was admitted to our clinic with a complaint of discoloration of both her brown irises. An ocular evaluation of the patient revealed symmetrical pigment deposition in trabecular meshwork. No iris transillumination defect, pupillary sphincter paralysis, keratic precipitates, and inflammatory reaction in anterior chamber were seen. The depigmented iris stroma became repigmented symmetrically after 3-year follow-up period. Although it is rare, BADI should be considered in the differential diagnosis of the diseases with bilateral iris depigmentation

The Effects of Fenvalerate on Hepatic and Cerebral Xenobiotic Metabolizing Enzymes in Selenium and/or Iodine Deficient Rats

Objective(s): Particularly in developing countries, selenium and/or iodine deficiencies are encountered and use of pesticides in agriculture are not well-controlled. Fenvalerate is a pyrethroid insectide used in agriculture and has applications against a wide range of pests. This study was designed to evaluate the effects of fenvalerate on hepatic and cerebral xenobiotic metabolizing enzyme activities in the presence of iodine and/or selenium deficiency on a rat model. Materials and Methods: Iodine and/or selenium deficiency was induced by feeding three-week-old Wistar rats with a diet containing <0.005 mg selenium kg-1, and/or administering 1% sodium perchlorate in drinking water for 7 weeks. Test groups received fenvalerate (100 mg kg-1 BW IP) for the last 7 days. Hepatic and cerebral microsomal aniline hydroxylase (CYP2E1) and cytosolic glutathione S-transferase (GST) activities were determined. Besides, hepatic NADPH-cytochrome P450 reductase (P450R), ethoxyresorufin O-deethylase (EROD, CYP1A1/1A2) and penthoxyresorufin O-depenthylase (PROD, CYP2B1/2B2), activities were also measured. Results: Fenvalerate had a general inductive effect on the hepatic and cerebral xenobiotic metabolizing enzyme activities. Moreover, enzyme activities were also altered by iodine and/or selenium deficiency, but the effects seemed to be enzyme- and tissue-specific. Conclusion: The inductive effect of fenvalerate, particularly in high dose exposures, may change the metabolism of several xenobiotics, including drugs, as well as endogenous substrates. The effects may vary depending on the selenium and/or iodine status of individual.PubMedWo