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Emergence of Antibiotic Resistance Genes sul1, tetA, blaGES, and mexF in Sapon Irrigation Canal and Aquaculture Pond in Kulon Progo Regency, Indonesia

Ikhrami Mohamad Aji, Sari Dini Wahyu Kartika, Putra Masagus Muhammad Prima

Journal of Ecological Engineering

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2024

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Vol. 25, nr 2

85--92

EN

Antibiotic resistance genes (ARGs) have recently become an emerging environmental contaminants. The aquatic environment, such as a river has already become the most polluted environment and can be a driver of ARGs. The water from irrigation canal has the potential to become a hotspot of ARGs through contamination from river pollutants carried along to the irrigation canal. However, the information regarding the cross-contamination of ARGs in fish farming systems integrated with irrigation canal in Indonesia needs further study. This study investigated the occurrence of ARGs sulfonamide (sul1), tetracycline (tetA), beta lactam (blaGES), and multi drug resistance (mexF) from body water samples along the irrigation canal and aquaculture ponds which utilize irrigation water for cultivation. Sampling sites are located in the Kulon Progo Regency (Indonesia) and samples were taken during the rainy season. Gene amplification was performed using Multiplex PCR. The results showed that sul1, tetA, and blaGES were detected in 67%, 63%, and 55% of all samples. Meanwhile, mexF was only found upstream and downstream irrigation canals, which accounted for 25% of the total samples. The results of this study indicated that the Sapon Irrigation Canal has the potential to cause the spread of antibiotic resistance genes.

2

New microsatellite multiplex PCR sets for genetic studies of the sterlet sturgeon, Acipenser ruthenus

Kohlmann K., Kersten P., Geßner J., Onără D., Taflan E., Suciu R.

Environmental Biotechnology

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2017

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Vol. 13, No. 1

11--17

EN

Wild populations of the sterlet sturgeon, Acipenser ruthenus, are declining throughout their native ranges. In-depth knowledge of their genetic diversity and structure is urgently needed to enable the identification of management units for conservation purposes. Moreover, genetic markers are required to establish appropriate breeding schemes for supportive stocking programs and to monitor genetic changes in farmed stocks. Therefore, six species-specific, polymorphic microsatellite loci were isolated and arranged into five multiplex PCR sets together with nine loci from other sturgeon species. The diversity of these 15 microsatellites was examined in 67 sterlet individuals (20 farmed in Germany and 47 wild-caught in the Romanian part of the River Danube). The total number of alleles per locus ranged from 3 to 15 with an average of 7.20. The farmed sterlet sturgeon possessed 1 to 7 alleles per locus, with a mean of 3.13; the wild individuals were more variable, with 3 to 15 alleles per locus and a mean of 7.07. Observed heterozygosities ranged from 0 to 0.850 in the farmed individuals, and from 0.064 to 0.957 in the wild individuals. Indications of inbreeding were only found in the wild sterlet sturgeon (FIS=0.062). The genetic differentiation of the two sterlet groups was significant (FST=0.1186). The high sensitivity and discriminatory power of the 15 loci was indicated by the very low overall probability of identity for siblings (PIsib=5.099x10-5) and the high accuracy of self-classification (66 out of the 67 individuals (98.51%) were correctly identified). Thus, these newly developed multiplex PCR sets are a valuable genetic tool for identifying management units for species conservation, sustainable fisheries and aquaculture.

3

Detection of meat adulteration in veal sausages using a multiplex PCR technique

Sawicki W., Żochowska-Kujawska J.

Biotechnology and Food Science

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2016

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Vol. 80, nr 1

19--27

EN

Previous methods used to detect veal contamination by lower value meat lacked easiness and accuracy This study describes a simple procedure for detecting origin of meat in processed meat products. A rapid (5h) protocol based on multiplex PCR was developed to detect undeclared chicken meat (a specific mitochondrial DNA sequence) in Polish veal sausages. Simultaneously a PCR assay was successfully optimized for amplification of 274-bp DNA fragment extracted from meat products using designed species-specific primer pairs for the detection of veal meat. This procedure also enabled differentiation of bovine or/and chicken meat from their less expensive porcine substitute.

4

New multiplex PCR assays for estimating genetic diversity in rainbow trout (Oncorhynchus mykiss) by polymorphism of microsatellite DNA

Kaczmarczyk D., Kaczor A.

Environmental Biotechnology

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2013

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Vol. 9, No. 1

19--24

EN

Multiplex PCR is a useful technique for estimating genetic diversity. This paper presents 3 new sets of primer pairs for effectively amplifying 10 microsatellite DNA loci from rainbow trout (Oncorhynchus mykiss). Unlike other sets of primer pairs that have been developed for amplifying rainbow trout microsatellite loci, ours do not require the hot-start PCR technique. In the paper, we describe the steps taken to choose the loci for each multiplex assay and to verify the genotyping results. We provide the compositions of the PCR mixture and the characteristics of the PCR thermal profile recommended for amplification.

5

Does egg sex ratio in Urban Kkestrels (Falco tinnunculus) differ from parity?

Rejt Ł., Gryczyńska-Siemiątkowska A., Rutkowski R., Malewska A.

Polish Journal of Ecology

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2005

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Vol. 53, nr 4

545-552

EN

Paper tests the hypothesis that urban kestrels (Falco tinnunculus) are sex biased connected with urbanization gradient (central zone vs suburbs), laying date and level of PCB-contamination. Blood samples of 158 nestlings were collected on FTA cards. Sex of nestlings was determined using a multiplex PCR technique. Egg sex ratio among kestrels in Warsaw (Poland) was 51% and did not differ significantly from parity (n = 34 nests). Among broods at the beginning and at the end of the breeding season proportion of males was significantly higher than in the middle of the season. Sex ratio was significantly different along the urbanization gradient. Proportion of males in broods at the central zone reached only 44% contrary to the external zone where males composed 65% of chicks. Possibly influence of laying date, female condition as well as population size and isolation is discussed. For assessing the level of PCBs small amount of blood (approximately 1 mm3) was collected from the brachial vein from 83 individuals (17 nests). All samples from a particular nest were pooled together to increase the possibility of successful analysis. Among most broods (pooled data for nests with complete and partial hatching) contamination of PCBs in nestlings. blood was low (average level of PCBs was 55.1 ppm, range: 0-252.8). A trend toward decreasing proportion of males among broods with higher PCB-contamination was found to be insignificant. Probably level of organic contamination in chicks. blood depends more on pollution existing in rural hunting areas and is not directly connected with nest site and its close vicinity.

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Analiza możliwości zastosowania metod sztucznej inteligencji w medycynie sądowej

Filipowicz E., Kwiecień J., Kłys M., Filipowicz B.

Bio-Algorithms and Med-Systems

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2005

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Vol. 1, no. 1/2

3--8

PL

Artykuł opisuje zastosowanie nowych systemów bioinformatycznych w medycynie sądowej. Systemy biometryczne już znalazły zastosowanie między innymi w geometrycznej identyfikacji twarzy. Są one niezbędne w identyfikacji osobowej oraz w poszukiwaniu osób zaginionych. W ostatnich latach nastąpił bardzo szybki rozwój badań nad chromosomem Y, co pozwoliło na postęp w medycynie sądowej. Metody sztucznej inteligencji mogąbyć pomocne w badaniach spornego ojcostwa i ewolucji człowieka. Bioinformatyka oraz metody biologii molekularnej, metody multiplex PCR będą pełnić bardzo ważną funkcję w analizie sądowej DNA oraz w historycznych i genealogicznych badaniach.

EN

This article reviews new bioinformatic systems in forensic medicine. Biometric systems are already used in forensic medicine for face geometry identification. They are necessary in personal identification and missing persons investigations. The field of Y-chromosome analysis and its application to forensic science has undergone rapid improvement in recent years. Artificial Intelligence is usefull in paternity testing and in human evolutionary study. Bioinformatic systems and multiplex PCR assay w ill play an important role in the future of forensic DNA typing and historical and genealogical research.