Hydrometeorological assessments of the transport of microplastic pellets in the Eastern Mediterranean.

Microplastic pellets were sampled in May and November 2018 during one-week surveys at 13 coastal beaches in Iskenderun Bay/Turkey. Pellet pollution index (PPI) was calculated for the beaches as a tool to assess beach pollution by microplastic pellets. Hydrometeorological conditions, including wind, current, wave, surface run-off, and precipitation, were examined during 2018 to reveal the effect on the transport of microplastic pellets within the study area. Sea-surface heights, including the astronomical tide and the storm surge and the wave runup heights, were also considered in the analysis to study the extent of hydrodynamic forcing on the beach. Hydrometeorological assessments indicated that the pellet concentrations in the coastal zone are mostly related to wind-induced transport. Three major river discharges are considered as the main source of microplastic pellets effluents. A Lagrangian particle transport model was conducted to reveal the possible beaching hotspots of microplastic pellets released from these river mouths. Average microplastic pellets were calculated as 126.04 ± 54.08 items/m2 for May 2018 and 70.22 ± 18.25 items/m2 for November 2018. An overall mean PPI for May 2018 was calculated as 1.13, indicating a moderate degree of pellet pollution, and 0.56 for November 2018, indicating a low degree of pellet pollution. The simulations showed that Orontes River effluents affected the inner Iskenderun Bay coasts more than the Seyhan and Ceyhan River.

[Lucifensin, Chymotrypsin Proteins and Molecular Characterization of Lucilia sericata]. / Lucilia sericata'nin Lusifensin, Kimotripsin Proteinleri ve Moleküler Karakterizasyonlari.

Lucilia sericata, one of the most common species of the Calliphoridae family, is found in large numbers around droppings, garbage and carcasses. This fly species is important in medicine, forensics and veterinary medicine. The larvae of the parasite are important both in veterinary medicine and in combating of the animal diseases, as they cause significant losses in animal production. Since they are one of the first fly colonies to settle on corpses, they can also be used in determining the time of death in the field of forensic medicine. L.sericata larvae used in Maggot debridement treatment (MDT) which is a treatment method with fly larvae, help wound healing by destroying necrotic tissues and infectious agents in wounds. While the larvae protect themselves from polymicrobial flora with the proteins they secrete; at the same time, they make an interesting contribution to wound healing with these molecules secreted. One of the most important molecules discovered in recent years is lucimycin which has an antifungal effect. In addition, lucifensin and chymotrypsin secretions have gained importance in recent years due to their antibacterial effects and especially their effects on resistant gram-negative and positive bacteria. There is a need for the discovery of the molecules that can be alternative in the treatment of non-healing wounds or that can be applied together with existing antibiotics. It is necessary to investigate the antimicrobial characterization of the compounds involved in maggot therapy and their mechanisms. The aim of this study was to clone, molecular characterization and analysis of the antigenic structures of lucifensin and chymotrypsin genes, which are important defensin molecules secreted by L.sericata larvae used in MDT. Primarily, the cultivation of L.sericata colonies to be used in molecular studies were performed. Later, RNA isolation and cDNA synthesis from larvae were carried out. Lucifensin and chymotrypsin genes were individually inserted into the pJet1.2 plasmid by cloning reactions. The presence of the recombinant plasmid was confirmed by PCR screening and DNA sequence analysis methods in all steps. Nucleotide and amino acid based molecular characterizations of these two genes, which are important larval components in wound treatment, have been made. Antigenic regions and three-dimensional structures of the proteins were obtained. The isolate numbered MT495795 of the L.sericata lucifensin gene and the isolate numbered MT495794 of the chymotrypsin gene were registered to GenBank. This data reported for the first time in the Republic of Turkey will contribute to the literature. From the beginning of the 20th century until the discovery of the antibiotics, MDT was applied especially on soldiers but did not find much application area after the discovery of the antibiotics. Drug resistance, which is the most important problem encountered in the treatment of the wounds today, has led to the recall of MDT and its mechanism of action. In this study the data, obtained will constitute a source for the multidisciplinary studies of the scientists from different fields on the discovery and applicability of the important moleculesin the treatment of the wounds.

[Plasmodium ovale malaria and molecular diagnosis: Could it be a relapse?] / Plasmodium ovale sitmasi ve moleküler tanisi: relaps olabilir mi?

Malaria caused by Plasmodium species continues to affect the half of the world population. According to the World Health Organization 2017 data, 445.000 cases of malaria and 219 million cases of new clinical malaria cases were reported during the year. African continent is the geographical region where the disease is most frequent. In recent years there has been an increase in the number of imported cases after travels to this continent. In this case report, relaps caused by Plasmodium ovale in a male Republic of Turkey citizen patient who has travelled to Uganda only and no other place a year and half ago was presented. Thin blood smear was prepared from the peripheral blood of the patient who admitted to our hospital with complaints of fever and chills. The smear was stained with Giemsa and examined with a x100 objective microscope and trophozoites belonging to Plasmodium genus were detected. Considering the size and locality of the trophozoites in the erythrocytes, it is thought that the parasite may be Plasmodium vivax. Nested PCR method was used for the species identification. Nested PCR studies were performed using Plasmodium genus and specific primers for P.vivax, Plasmodium falciparum, P.ovale and Plasmodium malariae. Nested PCR products were run on gel and P.ovale was visualized in 787 bp region. P.vivax, P.malariae, P.falciparum, P.ovale and Plasmodium knowlesi species specific primers and probe-based quantitative real-time PCR (qRt-PCR) study revealed that the patient was infected with P.ovale. The patient had no history of chronic illness but had a history of recovered malaria 7-8 years ago. The patient did not have any complaints other than these complaints. CMV IgM and IgG and Brucella aglutinisation tests were negative. It is clear that relapse cases can also be seen when P.ovale species are in hypnozoite stage in the liver. Although there are 18 reported cases of relapse in the last century, these phenomena do not provide sufficient evidence for the theory of relapse. A true relapse is thought to be mild symptoms and even subclinical disease. It is also known that it is difficult to distinguish a true recurrence in cases of relapses that can occur after a long time from primer infection. The best way to overcome this difficulty is to assume being in a malaria endemic area or not between primary infection and recurrence. We think that the applications that are carried out together with the microscope and molecular studies, especially in cases where there is relapses in which low parasitemia or travel story are insufficient, are extremely important both in terms of diagnosis and accurate identification of species and in the selection of treatment.

[Retrospective evaluation of serologic and molecular test results of toxoplasmosis suspected patients]. / Toxoplasmosis süpheli hastalara ait serolojik ve moleküler test sonuçlarinin retrospektif dlarak degerlendirilmesi.

Toxoplasma gondii is a compulsory intracellular protozoan parasite with a wide range of host in warm-blooded vertebrates and has importance in terms of health and economy. Toxoplasmosis is very common because it can infect people with a variety of ways; ingestion of contaminated water and nutrients; raw or undercooked meats containing tissue cysts, blood transfusions, organ transplantantation and transplacental transfer. The aim of this study was to evaluate serologic and molecular test results of toxoplasmosis pre-diagnosed patients. Anti-T.gondii-IgG, anti-T.gondii-IgM ELISA, anti-T.gondii-IgM IFAT and anti-T.gondii-IgG avidity serological tests and PCR tests were applied by using blood, cerebrospinal fluid, amniotic fluid, pericardial fluid and abscess samples from patients who have admitted to Erciyes University Faculty of Medicine Department of Parasitology routine serology and molecular diagnosis laboratories with a pre-diagnosis of toxoplasmosis. Among 6547 patients 3.3% (n= 220) were only IgM positive, 9.2% were both IgG and IgM positive (n= 598). Among male patients, the positivity rates were lower and only IgM seropositive patients were 0.6% (n= 45) while the frequency of both IgG and IgM positive patients was 0.8% (n= 47). The number of both IgG and IgM seropositive cases among new borns, constituting 6.4% (n= 425) of the total number of patients, was 20 (0.3%) and the number of IgM seropositive samples was 25 (0.4%). Only 290 patients positive for IgM antibodies were studied for IFAT and 22 of these patients were positive for anti-T.gondii-IFAT IgM. Anti-T.gondii IgG avidity test was performed in all IgG positive patients regardless of their IgM seropositivity; low avidity was found in 0.7% (n= 18) of IgM-negative patients' sera and equivocal avidity was detected in 6.5% (n= 179). Low avidity was detected in 2.6% of IgM positive patients. Nine of the patients evaluated as anti-T.gondii IgM negative and IgG positive were detected as positive by PCR and two of them were negative. One of these PCR-positive patient's amniotic fluid was sent after the serological test results and detected as positive. Twenty CSF samples were studied by PCR and 7 samples were positive. Also, 8 blood samples which were anti-T.gondii IgM negative and IgG positive were found to bepositive in 7 and negative in one sample with PCR results, subsequently. PCR tests with pericardial fluid and abscess materials were found to be negative. In the case of suspicious or risky situations such as false negatives or false positives resulting from cross-reaction that can occur in ELISA tests, unnecessary medication or interventional approaches can be avoided by applying molecular-based testing at laboratories with appropriate infrastructure. For this reason, we believe that the application of molecular tests in addition to serological tests in risky situations may give more reliable results.

How microplastics quantities increase with flood events? An example from Mersin Bay NE Levantine coast of Turkey.

Floods caused by heavy rain carry significant amounts of pollutants into marine environments. This study evaluates the effect of multiple floods that occurred in the northeastern Mediterranean region in Turkey between December 2016 and January 2017 on the microplastic pollution in the Mersin Bay. Sampling was repeated in four different stations both before and after the flood period, and it was determined that in the four stations, there was an average of 539,189 MPs/km2 before the flood, and 7,699,716 MPs/km2 afterwards, representing a 14-fold increase. Fourteen different polymer types were detected in an ATR FT-IR analysis, eight of which were not found in samples collected before the floods. The most common polymer type was identified as polyethylene both pre- and post-flood. The mean particle size, which was 2.37 mm in the pre-flood period, decreased to 1.13 mm in the post-flood period. A hydrodynamic modeling study was implemented to hindcast the current structure and the spatial and temporal distributions of microplastics within the study area. In conclusion, heavy rain and severe floods can dramatically increase the microplastic levels in the sea.

Fouling assemblage of benthic plastic debris collected from Mersin Bay, NE Levantine coast of Turkey.

The Mediterranean is an ecosystem that faces more and more microplastic pollution every day. This causes the whole of the Mediterranean to face the negative effects of plastic pollution. This study examines the state of plastic debris and fouling organisms found on it in one of the areas most affected by plastic pollution, Mersin Bay. As a result, a total of 3.88kg plastic (mean=0,97kg; n=120; 2670item/km2; 86,3kg/km2) was collected and based on the ATR-FTIR analysis, it was determined that this total contained 9 types of plastics. 17 different fouling species belonging to 6 phylum (Annelida, Arthropoda, Bryozoa, Chordata, Cnidaria, Mollusca) 7 class and 11 order were discovered on plastics. Spirobranchus triqueter, Hydroides sp. and Neopycnodonte cochlear were the most abundant species. In the end, the example of Mersin Bay shows that plastic debris as a substrate can contain a very high diversity of life just like natural substrates.

[Production and molecular characterization of Plasmodium falciparum recombinant circumsporozoite protein with 37 NANP and 4 NVDP epitopes]. / 37 NANP ve 4 NVDP epitoplu Plasmodium falciparum rekombinant circumsporozoite proteinin ekspresyonu ve moleküler karakterizasyonu.

Malaria is caused by the protozoan parasite Plasmodium, the leading cause of death amongst the parasitic diseases. The disease is transmitted to human by the bites of female Anopheles mosquitoes. According to the World Health Organization (WHO) data, there were an estimated 214 million malaria cases and estimated 438.000 deaths occurred worldwide, in 2015. It is observed that 90% of all the deaths due to malaria occur in Africa. 78% of these cases were children who are under five years old. Intensive malaria interventions helped to reduce malaria incidence by 37% between 2000 and 2015. Malaria is a curable disease if diagnosed and treated promptly and correctly. Drug resistance has developed against almost all anti-malarial drugs and an effective vaccine against malaria has not been developed yet. Vaccine studies initiated 40 years ago by sterile immunity against falciparum malaria through immunization by exposure to 1000 irradiated mosquitoes. Complex structures, complicated life cycles and various antigenic structures of Plasmodium species make vaccination studies difficult. Circumsporozoite protein (CSP), the most extensively studied protein is also present in the content of the vaccine candidate RTS,S which is currently closest to get license. CSP was the first described Plasmodium antigen because of its important role during initiation of the parasitic infection. CSP is the major surface coat protein of Plasmodium parasite. CSP is a soluble protein and recombinant form of the CSP can be produced in Escherichia coli. NANP repeat region is a target site for host antibodies. Recently many DNA, RNA and protein vaccine candidates are being developed against malaria. According to WHO, in the next 20 years period, malaria vaccine can be developed. In this study we aimed to produce recombinant CSP (rCSP). Initially, P.falciparum CSP gene was amplified by PCR. CSP gene was cloned in to the pJET cloning vector. The gene subcloned to the pET100 protein expression vector. E.coli cells were used for protein expression. After this process, purification and endotoxin removal protocols were performed. As a result, 1182 bp CSP gene was obtained from P.falciparum genomic DNA. Accuracy of cloning and DNA sequence of the CSP gene was determined with DNA sequence analysis. The gene sequence was recorded to the GenBank with a registration no KT315396. rCSP was expressed in E.coli cells. The existence of rCSP was verifiedwith Western Blot method and was purified and removed from endotoxins. rCSP aminoacid sequence and 3D shape was obtained.We believe that the production of recombinant CSP will enable us to contribute to the further malaria vaccine studies in our laboratory and country.

[Molecular characterization of Echinococcus granulosus isolates obtained from different hosts]. / Farkli konaklardan elde edilen Echinococcus granulosus izolatlarinin moleküler karakterizasyonu.

Echinococcus granulosus is a parasite that can be seen throughout the world. So far, five species of genus Echinococcus have been identified as parasite in people: E.granulosus, E.multilocularis, E.vogeli, E.oligarthrus, E.shiquicus. Larval (metacestod) form of parasite settles in internal organs of hoofed animals (cattle, goats, pigs, horses, sheep, etc.) and human; the adult form is found in small intestine of final host, canine. Disease caused by parasite called as "Cystic echinococcosis" (CE) is an important health problem and causes economic losses in many countries including our country that livestock is common. Infective eggs cause infections in intermediate hosts by taking oral way and rarely inhalation. Received egg opens in the stomach and intestines of intermediate host and oncosphere is released. Oncosphere quickly reaches the lamina propria of the villus epithelium by its histolytic enzymes and hooks. It usually transported from here to the liver and lungs, less frequently, muscle, brain, spleen, kidney and to other organs through the veins. By molecular studies, five species have been validated taxonomically and 10 different variants or strains of E.granulosus have been identified. Host and developmental differences between strains may negatively affect control studies and fight against the parasite. This study aimed to determinate E.granulosus strains obtained from cyst material of different intermediate hosts from different regions of Turkey by molecular methods. In the study, 25 human, 8 cattle, 6 sheep and 2 goat cysts material has been collected. Total genomic DNA was isolated from protoscoleces in cyst fluid and analyzed by PCR with COX-1 (L) and COX-1 (S) genes specific primers. DNA sequence analysis for each PCR product has been made. DNA sequence analysis results evaluated phylogenetically by MEGA analyze and BLAST software. As a result of this study, all isolates were identified as E.granulosus sensu stricto (G1) by DNA sequence analysis. CE is a major public health problem for our country so we believe that obtained data from this study is an important source for parasite control, effective diagnosis, treatment techniques, eradication, vaccination and drug development. Similar studies will be beneficial to cover all other regions of Turkey and to develop effective and successful control programs.

Synthesis of imine bond containing insoluble polymeric ligand and its transition metal complexes, structural characterization and catalytic activity on esterification reaction.

In this study, synthesis of insoluble polymeric ligand (L) and its transition metal complexes [Cu(L)Cl2]·2H2O (1), [Co(L)Cl2(H2O)2] (2) and [Ni(L)Cl2(H2O)2] (3), having the azomethine groups, were synthesized by the condensation reactions of the diamines and dialdehydes. The structural properties were characterized by the analytical and spectroscopic methods using by elemental analysis, Fourier Transform Infrared, Thermo Gravimetric Analysis, Powder X-ray Diffraction, magnetic susceptibility and Inductively Coupled Plasma. The solubilities of the synthesized polymeric materials were also investigated and found as insoluble some organic and inorganic solvents. Additionally, their catalytic performance was carried out for the esterification reaction of acetic acid and butyl acetate. The highest conversion rate is 75.75% by using catalyst 1. The esterification of butanol gave butyl acetate with 100% selectivity.

Cloning of the DNA Vaccine Candidate LACK Gene of Leishmania infantum.

OBJECTIVE: Leishmaniasis is caused by an obligate intracellular protozoa belonging to Leishmania genus and listed among major tropical diseases by WHO. Because of the high costs, toxicity, and adverse effects of routinely used compounds in the treatment, alternative treatment and vaccine studies are underway. An effective vaccine has not been developed to date. In this study, we aimed to clone one of the most promising DNA vaccine candidates: the homolog-activated C kinase (LACK) gene of Leishmania infantum. METHODS: L. infantum genomic DNA was isolated from promastigote culture. The LACK gene was placed into plasmid pJET1.2. Then, recombinant plasmids were transformed into competent cells. The presence of recombinant plasmids was determined by PCR screening. Cloning was confirmed by PCR, restriction enzyme assays, and finally, DNA sequence analysis, after making miniprep from positive colonies. RESULTS: After performing PCR with LACK-gene specific primers, 939-bp PCR products were observed. Recombinant plasmids, which were transformed into competent Escherichia coli cells, were verified by PCR screening. It was verified by PCR that the recombinant plasmid contained the LACK gene. DNA sequence analysis was performed to obtain the DNA sequence. CONCLUSION: One of the most promising DNA vaccine candidates against leishmaniasis, the LACK gene, was cloned in this study.

Microbiota: In Health and in Sickness, From Birth to Death.

Microorganisms colonize tissues and organs such as the skin and gastrointestinal, respiratory, and genitourinary systems. These microorganisms are generally called as "human microbiota". Human microbiota mostly consists of commensal microorganisms. The commensal microorganisms located on and in the human body are bacteria, fungi, viruses, archaea, and parasites. The microbiota genome is 100 times bigger in size than the human genome. Although the human genome is stationary, microbial genome has a compatible flexible variability during human life. As well as 2-year-old child and newborn, adult and adolescent, the elderly and pregnant woman have a different microbiota. Microbiota and the microbiota genome can be changed by personal and household diet, antibiotic use, mode of delivery, and hygiene within days or even hours, depending on such as these factors. The human immune system and microbiota grow up, develop, and mature as childhood friends by playing with each other from birth to death. Association between microbiota and human is not just related to childhood-it continues with health and disease, until death separates them. This review focused on the roles of microbiota in parasitology, autoimmune diseases, metabolic diseases, and cancer treatment in detail. In addition, inflammatory and immunoregulatory roles of microbiota on the intestinal immune system and how innate and adaptive immune systems regulate microbiota and its content were explained.

[Cloning DNA Vaccine Candidate SAG1 Gene of Toxoplasma gondii]. / Toxoplasma gondii DNA Asisi Adayi SAG1 Geninin Klonlanmasi.

OBJECTIVE: Toxoplasma gondii, which is observed in our country and worldwide, can cause mortality and is an important public health problem because of engaging babies from pregnant women. An effective vaccine against toxoplasmosis has not yet been developed. SAG1 protein is released from the bradyzoites and tachyzoites stages of T. gondii and is important at the pathogenesis of the disease. This study aimed to clone a promising DNA vaccine candidate, SAG1 gene, of T. gondii. METHODS: T. gondii genomic DNA was isolated from tachyzoites of T. gondii. SAG1 gene was amplified with specific primers and then cloned into the pJET1.2 vector. Recombinant plasmids were transformed into Escherichia coli cells. The presence of recombinant plasmids was determined by polymerase chain reaction (PCR) screening. Following the purification of the recombinant plasmid from positive colonies, cloning was confirmed by PCR, restriction enzyme assays, and DNA sequence analysis. RESULTS: After PCR with SAG1 gene-specific primers, 1010-bp PCR products were obtained. Recombinant plasmid, which was transformed into competent E. coli cells, was verified by PCR screening. Moreover, PCR verified that the recombinant plasmids contained the SAG1 gene. The DNA sequence was analyzed, and the DNA sequence was obtained. CONCLUSION: One of the promising DNA vaccine candidates against toxoplasmosis, SAG1 gene, has been cloned.