Discrimination of Cricotopus species (Diptera: Chironomidae) by DNA barcoding

2008 ◽  
Vol 98 (6) ◽  
pp. 555-563 ◽  
Author(s):  
C.S. Sinclair ◽  
S.E. Gresens
Keyword(s):  
Water Quality ◽  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Mitochondrial Gene ◽  
Accurate Method ◽  
Taxonomic Resolution ◽  
Molecular Approaches ◽  
Putative Species ◽  
Sequence Variations ◽  
Wide Range

AbstractChironomids (Diptera) typically comprise the most abundant group of macroinvertebrates collected in water quality surveys. Species in the genus Cricotopus display a wide range of tolerance for manmade pollutants, making them excellent bioindicators. Unfortunately, the usefulness of Cricotopus is overshadowed by the difficulty of accurately identifying larvae using current morphological keys. Molecular approaches are now being used for identification and taxonomic resolution in many animal taxa. In this study, a sequence-based approach for the mitochondrial gene, cytochrome oxidase I (COI), was developed to facilitate identification of Cricotopus species collected from Baltimore area streams. Using unique COI sequence variations, we developed profiles for seven described Cricotopus sp., four described Orthocladius sp., one described Paratrichocladius sp. and one putative species of Cricotopus. In addition to providing an accurate method for identification of Cricotopus, this method will make a useful contribution to the development of keys for Nearctic Cricotopus.

scholarly journals Pollen DNA barcoding: current applications and future prospects

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 629-640 ◽  
Author(s):  
Karen L. Bell ◽  
Natasha de Vere ◽  
Alexander Keller ◽  
Rodney T. Richardson ◽  
Annemarie Gous ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Plant Communities ◽  
Taxonomic Resolution ◽  
Future Research ◽  
Future Prospects ◽  
Species Origin ◽  
Research Programs ◽  
Wide Range ◽  
New Applications ◽  
Plant Pollinator

Identification of the species origin of pollen has many applications, including assessment of plant–pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.

scholarly journals Molecular Identification of Mudskipper Fish (Periophthalmus spp.) from Baros Beach, Bantul, Yogyakarta

2021 ◽  
Vol 6 (3) ◽  
pp. 66391
Author(s):  
Katon Waskito Aji ◽  
Tuty Arisuryanti
Keyword(s):  
Genetic Distance ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Fish Species ◽  
Mitochondrial Gene ◽  
Universal Primers ◽  
Molecular Approaches ◽  
Morphological Studies ◽  
The Family ◽  
Pcr Method

Mudskipper fish is amphibious fish belonging to the family Gobiidae. Coastal communities widely consume mudskipper to meet their animal protein needs. Mudskipper is primarily cryptic species that are morphologically difficult to identify and distinguish from other mudskipper fish species. Consequently, it can be confused with the naming of mudskipper fish species and can affect the conservation efforts of the fish in their habitat. One of the molecular approaches that can be used to identify the fish species quickly and accurately is DNA barcoding using the COI mitochondrial gene. However, the research on the identification of mudskipper fish in Indonesia is still very limited. Therefore, this study aimed to identify 26 mudskipper fish from Baros Beach, Bantul, Yogyakarta, using COI mitochondrial gene as a molecular marker for DNA barcoding. The method used in this study was a PCR method with universal primers, FishF2 and FishR2. The data obtained were then analyzed using GeneStudio, DNASTAR, BLAST, Identification Engine, Mesquite, MEGAX, and BEAST. The analysis was conducted to obtain similarity, genetic distance and reconstruct a phylogenetic tree. The result revealed that all 26 samples of mudskippers collected from Baros Beach were identified in one genus, namely Periophthalmus, and consisted of 3 species, namely P. kalolo (16 samples), P. argentilineatus (9 samples), and P. novemradiatus (1 sample). Furthermore, this study also discovered a suspected cryptic species in P. argentilineatus with a genetic distance of 5.46-5.96% between clade E, F compared with clade G. Further morphological studies are needed to confirm the species status of these three clades before solidly proclaim that they are cryptic species. 

DNA BARCODING FOR IDENTIFICATION OF PROCESSED TUNA FISH IN INDONESIAN MARKET

2016 ◽  
Vol 78 (4-2) ◽  
Author(s):  
Mala Nurilmala ◽  
Utut Widyastuti ◽  
Wisnu Ananta Kusuma ◽  
Nurjanaha Nurjanaha ◽  
Nuring Wulansari ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Cytochrome B ◽  
Mitochondrial Gene ◽  
Free Trade Area ◽  
Accurate Method ◽  
Molecular Technique ◽  
Direct Sequence ◽  
Tuna Fish ◽  
Trade Area ◽  
Canned Tuna

DNA barcoding is a molecular technique to characterize species organism using a short DNA sequence. Recently, it becomes useful tool to detect seafood mislabeling and species substitution. Cytochrome b is one of the mitochondrial gene used in DNA barcoding. In order to face the regulation of AFTA (ASEAN Free Trade Area), the accurate method to detect the fish species and its products is needed in order to avoid the fraudulent in Indonesia. Thus, an attempt was carried out to identify authentication for tuna’s products (sushi, fish ball, meat floss, and canned tuna). The samples were collected from, Bogor, West Java, Indonesia. DNA was isolated according to the manufacturer’s protocol. The amplification of DNA by PCR was carried out, then the direct sequence was performed. In the present study, DNA barcoding of tuna’s product using cytochrome b were elucidated. The amplification of DNA by PCR was successfully obtained from tuna’s sample except one of canned tuna (K3). It showed that one of the canned tuna as in the label did not contain tuna. It indicated that there was an economic fraud for one of canned tuna.

scholarly journals First record of hagfish (Cyclostomata: Myxinidae) in Indian waters

2017 ◽  
Vol 9 (6) ◽  
pp. 10365
Author(s):  
B. Fernholm ◽  
A. Biju Kumar ◽  
Michael Norén
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome Oxidase ◽  
Arabian Sea ◽  
High Probability ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
First Record ◽  
Putative Species ◽  
Kerala Coast ◽  
Indian Waters

One specimen of hag fish Eptatretus sp. was collected from the Arabian Sea, off Kerala coast of India at 500-600 m depth. The phylogenetic analysis using the sequence of mitochondrial gene cytochrome oxidase C (CO1) suggested the Eptatretus sp. collected from India is distinct from all other species where sequence data is available and P ID (Liberal) for Eptatretus sp. collected from India is 0.96, indicating a high probability that an unknown member of the putative species would be correctly identified as a member once more specimens are collected.

scholarly journals Advances and Applications of Water Phytoremediation: A Potential Biotechnological Approach for the Treatment of Heavy Metals from Contaminated Water

2021 ◽  
Vol 18 (10) ◽  
pp. 5215
Author(s):  
Cristián Raziel Delgado-González ◽  
Alfredo Madariaga-Navarrete ◽  
José Miguel Fernández-Cortés ◽  
Margarita Islas-Pelcastre ◽  
Goldie Oza ◽  
...  
Keyword(s):  
Water Quality ◽  
Plant Species ◽  
Treatment Strategies ◽  
Pollution Sources ◽  
Water Contaminants ◽  
Biotechnological Approach ◽  
Wide Range ◽  
Great Relevance ◽  
Multidisciplinary Perspective ◽  
Viable Method

Potable and good-quality drinking water availability is a serious global concern, since several pollution sources significantly contribute to low water quality. Amongst these pollution sources, several are releasing an array of hazardous agents into various environmental and water matrices. Unfortunately, there are not very many ecologically friendly systems available to treat the contaminated environment exclusively. Consequently, heavy metal water contamination leads to many diseases in humans, such as cardiopulmonary diseases and cytotoxicity, among others. To solve this problem, there are a plethora of emerging technologies that play an important role in defining treatment strategies. Phytoremediation, the usage of plants to remove contaminants, is a technology that has been widely used to remediate pollution in soils, with particular reference to toxic elements. Thus, hydroponic systems coupled with bioremediation for the removal of water contaminants have shown great relevance. In this review, we addressed several studies that support the development of phytoremediation systems in water. We cover the importance of applied science and environmental engineering to generate sustainable strategies to improve water quality. In this context, the phytoremediation capabilities of different plant species and possible obstacles that phytoremediation systems may encounter are discussed with suitable examples by comparing different mechanistic processes. According to the presented data, there are a wide range of plant species with water phytoremediation potential that need to be studied from a multidisciplinary perspective to make water phytoremediation a viable method.

scholarly journals 264 Effects of Water Quality on Nursery Pig Performance and Health

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 89-89
Author(s):  
Brigit Lozinski ◽  
Brent Frederick ◽  
Adrienne Hilbrands ◽  
Yuzhi Li ◽  
Milena Saqui-Salces ◽  
...  
Keyword(s):  
Water Quality ◽  
Experimental Unit ◽  
Respiratory Syndrome Virus ◽  
Chi Square ◽  
Wide Range ◽  
Mycoplasma Pneumonia ◽  
Quality Water ◽  
Pig Performance ◽  
Chi Square Analysis ◽  
Water Treatments

Abstract Newly-weaned pigs (n = 450; age = 20 d) were used in a 40-d experiment to determine the effects of water quality on pig performance and health. Pigs were sourced from a single commercial sow farm that was negative for both Porcine Reproductive and Respiratory Syndrome virus and Mycoplasma Pneumonia. Pigs were allotted randomly to 45 pens (10 pigs/pen) and pens were assigned to 1 of 3 water treatments that provided water of differing quality. Waters were selected to represent a wide range of perceived water quality. Water quality was determined based on concentration of analytes including sulfates (1,120; 617; 2 ppm), iron (5.4; 5.2; 1.3 ppm), Total Dissolved Solids (TDS; 1,500; 1,050; 348 ppm), hardness (1,410; 909; 235 mg Eq CaCO3/L), magnesium (171; 91; 21 ppm) and sodium (64; 37; 29 ppm) for waters A, B, and C, respectively. Pigs were housed in an environmentally controlled, power ventilated, confinement nursery barn and were allowed ad libitum access to a common three-phase diet and water across all water treatments. Weekly ADG, ADFI, and G:F were measured and subjective scour score (1=solid feces to 4=liquid feces) was recorded daily through day 7. Data for pig growth performance were analyzed using PROC GLIMMIX with water quality as a fixed effect and pen served as the experimental unit. There were no differences among treatments in ADG, ADFI, and G:F (Table 1). Number of pigs treated with antibiotics throughout the experiment did not differ among treatments as determined by Chi-Square analysis. Average subjective scour score on day 7 of the experiment also did not differ among treatments. In conclusion, performance and health of nursery pigs as measured in this experiment were not influenced by the differing water qualities studied.

scholarly journals Molecular Subtyping of Blastocystis sp. Isolated from Farmed Animals in Southern Italy

2021 ◽  
Vol 9 (8) ◽  
pp. 1656
Author(s):  
Simona Gabrielli ◽  
Marialetizia Palomba ◽  
Federica Furzi ◽  
Emanuele Brianti ◽  
Gabriella Gaglio ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Pcr Amplification ◽  
Epidemiological Studies ◽  
Fallow Deer ◽  
Small Subunit ◽  
Zoonotic Transmission ◽  
Ssu Rrna ◽  
Molecular Approaches ◽  
Wide Range ◽  
Blastocystis Sp

Blastocystis is a common intestinal protist distributed worldwide, infecting humans and a wide range of domestic and wild animals. It exhibits an extensive genetic diversity and, so far, 25 distinct small subunit ribosomal RNA (SSU rRNA) lineages termed subtypes (STs)) have been characterized; among them, 12 have thus far been reported in humans. The aims of the present study were to detect and genetically characterize Blastocystis sp. in synantropic animals to improve our current knowledge on the distribution and zoonotic transmission of Blastocystis STs in Italy. Samples were collected from N = 193 farmed animals and submitted to DNA extraction and PCR amplification of the SSU rRNA. Blastocystis was detected in 60 samples (31.08%) and successfully subtyped. Phylogenetic analysis evidenced that the isolates from fallow deer, goats, and pigs (N = 9) clustered within the ST5; those from pheasants (N = 2) in the ST6; those from chickens (N = 8) in the ST7; those from sheep (N = 6) in the ST10; and those from water buffaloes (N = 9) in the ST14 clade. The comparison between the present isolates from animals and those previously detected in humans in Italy suggested the animal-to-human spillover for ST6 and ST7. The present study represents the widest Blastocystis survey performed thus far in farmed animals in Italy. Further epidemiological studies using molecular approaches are required to determine the occurrence and distribution of Blastocystis STs in other potential animal reservoirs in Italy and to define the pathways of zoonotic transmission.

scholarly journals Phylogeographic Investigation of an Endangered Longhorn Beetle, Callipogon relictus (Coleoptera: Cerambycidae), in Northeast Asia: Implications for Future Restoration in Korea

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 555
Author(s):  
Ji-Hyoun Kang ◽  
Dae-Am Yi ◽  
Alexander V. Kuprin ◽  
Chang-Do Han ◽  
Yeon-Jae Bae
Keyword(s):  
South Korea ◽  
Mitochondrial Gene ◽  
Northeast Asia ◽  
Haplotype Network ◽  
Conservation Strategies ◽  
Genetic Characteristics ◽  
Linear Pattern ◽  
Wide Range ◽  
Longhorn Beetle ◽  
High Level

The longhorn beetle, Callipogon (Eoxenus) relictus Semenov, is the only remnant species found in the Palearctic region, while all other Callipogon species are distributed mainly in Central America and partly in South America. This species has been placed in the first category (as ‘critically endangered’) of the Red Data Book in Russia and designated as one of the top-priority target species among all endangered invertebrate species for restoration in South Korea since 2006. Although its restricted distribution in Northeast Asia with a high conservational value has been highlighted, genetic features of C. relictus from different geographic regions remain unexplored. We first investigated the level of genetic diversity and phylogeographic patterns of C. relictus to evaluate the current conservational status and the feasibility of the implementation of a restoration program. The average genetic divergence of mitochondrial gene COI based on Kimura-2-parameter distance among the four regions in Russia, China, North Korea, and South Korea was 2.2%, which lies within the range of intraspecific levels. However, two separate clades with 3.8% divergence were identified, despite no geographical clustering of haplotypes. The linear pattern of the haplotype network with a high level of haplotype and nucleotide diversities suggests that the wide range of currently fragmented populations might be the remnant of genetically diverse populations in the past. This study will provide crucial information on the genetic characteristics and phylogeographic history of C. relictus, which will help to establish conservation strategies for this cherished insect species in Northeast Asia.

scholarly journals Recovering Forecast Distributions of Crop Composition: Method and Application to Kentucky Agriculture

2020 ◽  
Vol 12 (7) ◽  
pp. 2917
Author(s):  
GwanSeon Kim ◽  
Mehdi Nemati ◽  
Steven Buck ◽  
Nicholas Pates ◽  
Tyler Mark
Keyword(s):  
Water Quality ◽  
Land Use ◽  
Transition Probabilities ◽  
New Crops ◽  
Run Off ◽  
Wide Range ◽  
Data Layer ◽  
Mnl Model ◽  
Total Acreage ◽  
Specific Capital

This paper proposes a novel application of the multinomial logit (MNL) model using Cropland Data Layer and field-level boundaries to estimate crop transition probabilities, which are used to generate forecast distributions of total acreage for five major crops produced in the state of Kentucky. These forecasts distributions have a wide range of applications that, besides providing interim acreage estimates ahead of the June Acreage Survey, can inform the ability of producers to incorporate new crops in the land-use rotation, investments in location-specific capital and input distribution as well informing the likelihood of adverse water quality events from nutrient run-off.

Sign in / Sign up

Export Citation Format

Share Document