DNA barcoding and phylogenetic relationship of shrimps (Crustacea: Decapoda) of Bangladesh

We adopted DNA barcoding technique using a 658-bp fragment of the mitochondrial cytochrome c oxidase I (COI) gene to identify shrimp species collected from the different areas of Bangladesh. A total of 24 sequences were generated belonging to 14 species including four new records- Macrobrachium nipponense, Macrobrachium kistnense, Exopalaemon carinicauda and Alpheus malleator. Genetic distance measured with Kimura 2 parameter showed that genetic divergence increased with higher taxonomic rank. The mean genetic divergence was evaluated and found to be 0.935%, 22.67% and 30.92% within species, genus and family, respectively. In addition to the barcode-based species identification system, phylogenetic relationships were established where individuals belonging to the same species were grouped under the same clade. Maximum likelihood (ML) was preferred as the statistical method and as expected, the phylogenetic tree complemented and ensured the conventional taxonomy. The present study evidently showed that DNA barcoding can be served as an effective tool to discriminate the shrimp species and this will enhance the understanding on evolution and conservation biology. Bioresearch Commu. 7(1): 941-946, 2021 (January)

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Species Delimitation of Scavenger Flies in the Valley of Mexico

Journal of Medical Entomology ◽

10.1093/jme/tjab094 ◽

2021 ◽

Author(s):

Carlos Pedraza-Lara ◽

Marco A Garduño-Sánchez ◽

Isabel Téllez-García ◽

Stephany Rodríguez-González ◽

Eduardo Nuple-Juárez ◽

...

Keyword(s):

Species Richness ◽

Dna Barcoding ◽

Species Delimitation ◽

Nature Reserve ◽

New Records ◽

Dna Barcode ◽

Coi Gene ◽

Baseline Knowledge ◽

Identification Of Species ◽

Diverse Groups

Abstract Identification of species involved in cadaveric decomposition, such as scavenger Diptera, is a fundamental step for the use of entomological evidence in court. Identification based on morphology is widely used in forensic cases; however, taxonomic knowledge of scavenger fauna is poor for many groups and for many countries, particularly Neotropical ones. A number of studies have documented the utility of a DNA barcoding strategy to assist in the identification of poorly known and diverse groups, particularly in cases involving immature states or fragmented organisms. To provide baseline knowledge of the diversity of scavenger Diptera in the Valley of Mexico, we generated a DNA barcode collection comprised of sequences of the cytochrome c oxidase subunit 1 (COI) gene for all families sampled at a nature reserve located in this region. We collected and identified specimens on the basis of morphology and a species delimitation analysis. Our analyses of 339 individuals delineated 42 species distributed across nine families of Diptera. The richest families were Calliphoridae (9 species), Sarcophagidae (7 species), and Phoridae (6 species). We found many of the species previously recorded for the Valley of Mexico, plus 18 new records for the region. Our study highlights the utility of DNA barcoding as a first-step strategy to assess species richness of poorly studied scavenger fly taxa.

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Molecular diversity of freshwater fishes of Bangladesh assessed by DNA barcoding

Bangladesh Journal of Zoology ◽

10.3329/bjz.v48i1.47872 ◽

2020 ◽

Vol 48 (1) ◽

pp. 1-19

Author(s):

Md Sagir Ahmed ◽

Sujan Kumar Datta ◽

Ayesha Akhter Zhilik

Keyword(s):

Dna Barcoding ◽

High Efficiency ◽

Gc Content ◽

Freshwater Fishes ◽

Coi Gene ◽

P Value ◽

Base Pairs ◽

Mitochondrial Coi ◽

Interspecific Distance ◽

The Mean

This study represents the comprehensive molecular identification of freshwater fishes of Bangladesh based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome. A total of 315 mitochondrial COI barcode sequences were obtained from 153 species,114 genera, 49 families and 16 orders of fishes. The mean length of the sequences was 652 base pairs. For all the samples, %G was significantly lower compared to the other nucleotides and %GC was lower compared to %AT (p-value ˂ 0.05). Also, a significantly lower %GC content was observed in second and third codon position compared to the first one in all the samples (1st>2nd>3rd, p-value˂ 0.05). The average K2P distances within species, genera, families and orders were 0.38%, 7.02%, 12.75% and 18.68%, respectively. The mean interspecific distance was 18-fold higher than the mean intraspecific distance. The K2P neighbor-joining (NJ) trees based on the sequences generally clustered species according to their taxonomic position. A total of 12 species were newly recorded in Bangladesh. High efficiency in species identification were demonstrated in the present study by DNA barcoding, and concluded that COI sequencing can be used as an authentic identification marker for freshwater fish species. Bangladesh J. Zool. 48(1): 1-19, 2020

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DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria

F1000Research ◽

10.12688/f1000research.7895.1 ◽

2016 ◽

Vol 5 ◽

pp. 1268 ◽

Cited By ~ 7

Author(s):

Mofolusho O. Falade ◽

Anthony J. Opene ◽

Otarigho Benson

Keyword(s):

16S Rrna ◽

Dna Barcoding ◽

Phylogenetic Trees ◽

Genetic Relationships ◽

Clarias Gariepinus ◽

Coi Gene ◽

Identification System ◽

Rrna Gene ◽

Oxidase Subunit ◽

Sarotherodon Melanotheron

DNA barcoding has been adopted as a gold standard rapid, precise and unifying identification system for animal species and provides a database of genetic sequences that can be used as a tool for universal species identification. In this study, we employed mitochondrial genes 16S rRNA (16S) and cytochrome oxidase subunit I (COI) for the identification of some Nigerian freshwater catfish and Tilapia species. Approximately 655 bp were amplified from the 5′ region of the mitochondrial cytochrome C oxidase subunit I (COI) gene whereas 570 bp were amplified for the 16S rRNA gene. Nucleotide divergences among sequences were estimated based on Kimura 2-parameter distances and the genetic relationships were assessed by constructing phylogenetic trees using the neighbour-joining (NJ) and maximum likelihood (ML) methods. Analyses of consensus barcode sequences for each species, and alignment of individual sequences from within a given species revealed highly consistent barcodes (99% similarity on average), which could be compared with deposited sequences in public databases. The nucleotide distance between species belonging to different genera based on COI ranged from 0.17% between Sarotherodon melanotheron and Coptodon zillii to 0.49% between Clarias gariepinus and C. zillii, indicating that S. melanotheron and C. zillii are closely related. Based on the data obtained, the utility of COI gene was confirmed in accurate identification of three fish species from Southwest Nigeria.

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DNA barcode of Parodontidae species from the La Plata river basin - applying new data to clarify taxonomic problems

Neotropical Ichthyology ◽

10.1590/s1679-62252013000300003 ◽

2013 ◽

Vol 11 (3) ◽

pp. 497-506 ◽

Cited By ~ 21

Author(s):

Elisangela Bellafronte ◽

Tatiane Casagrande Mariguela ◽

Luiz Henrique Garcia Pereira ◽

Claudio Oliveira ◽

Orlando Moreira-Filho

Keyword(s):

Genetic Distance ◽

Dna Barcoding ◽

Genetic Divergence ◽

Dna Barcode ◽

Molecular Data ◽

Efficient Tool ◽

La Plata ◽

La Plata Basin ◽

Close Relationship ◽

The Mean

In the past years, DNA barcoding has emerged as a quick, accurate and efficient tool to identify species. Considering the difficulty in identifying some Parodontidae species from the La Plata basin and the absence of molecular data for the group, we aimed to test the effectiveness of DNA barcoding and discuss the importance of using different approaches to solve taxonomic problems. Eight species were analyzed with partial sequences of Cytochrome c oxidase I. The mean intraspecific K2P genetic distance was 0.04% compared to 4.2% for mean interspecific K2P genetic distance. The analyses of distance showed two pairs of species with K2P genetic divergence lower than 2%, but enough to separate these species. Apareiodon sp. and A. ibitiensis, considered as the same species by some authors, showed 4.2% genetic divergence, reinforcing their are different species. Samples of A. affinis from the Uruguay and Paraguay rivers presented 0.3% genetic divergence, indicating a close relationship between them. However, these samples diverged 6.1% from the samples of the upper Paraná River, indicating that the latter represents a potentially new species. The results showed the effectiveness of the DNA barcoding method in identifying the analyzed species, which, together with the morphological and cytogenetic available data, help species identification.

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Italian Odonates in the Pandora’s Box: A Comprehensive DNA Barcoding Inventory Shows Taxonomic Warnings at the Holarctic Scale

10.1101/2020.04.23.056911 ◽

2020 ◽

Author(s):

Andrea Galimberti ◽

Giacomo Assandri ◽

Davide Maggioni ◽

Fausto Ramazzotti ◽

Daniele Baroni ◽

...

Keyword(s):

Cryptic Species ◽

Dna Barcoding ◽

Genetic Divergence ◽

Species Delimitation ◽

Coi Gene ◽

Dna Barcodes ◽

Mitochondrial Coi ◽

Haplotype Networks ◽

Mitochondrial Coi Gene

AbstractThe Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference datasets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658 bp 5’ end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the dataset to 1294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC, bGMYC) methods were used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct Molecular Operational Units, whereas the remaining ones were classified as ‘warnings’ (i.e., showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped in three categories depending on if they showed low, high, or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic, and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.

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Grunts (Actinopterygii: Perciformes: Haemulidae) of Bangladesh with two new distributional records from the northern Bay of Bengal assessed by morphometric characters and DNA barcoding

Acta Ichthyologica Et Piscatoria ◽

10.3897/aiep.51.67043 ◽

2021 ◽

Vol 51 (3) ◽

pp. 299-309

Author(s):

Kazi Ahsan Habib ◽

Md Jayedul Islam ◽

Najmun Nahar ◽

Mohammad Rashed ◽

Amit Kumer Neogi ◽

...

Keyword(s):

Dna Barcoding ◽

Bay Of Bengal ◽

Mangrove Forest ◽

New Records ◽

Coi Gene ◽

Morphometric Characters ◽

Commercially Important ◽

Northern Bay Of Bengal ◽

Sundarbans Mangrove ◽

The Sundarbans

Grunts (family Haemulidae) are among the most commercially important fish in Bangladesh. This paper provides brief diagnostic characters of five previously reported grunt species: Plectorhinchus pictus (Thunberg, 1792); Pomadasys andamanensis McKay et Satapoomin, 1994; Pomadasys argenteus (Forsskål, 1775); Pomadasys argyreus (Valenciennes, 1833); Pomadasys maculatus (Bloch, 1793) and two new distributional records: Pomadasys guoraca (Cuvier, 1829) and Plectorhinchus macrospilus Satapoomin et Randall, 2000. The fishes were collected from the Saint Martin’s Island coral reef-like ecosystem and the adjacent sea of the Sundarbans mangrove forest of Bangladesh. The examined specimens were identified and diagnosed based on their morphometric characters and DNA barcoding COI gene. The new records of Pomadasys guoraca and Plectorhinchus macrospilus from Bangladesh greatly extend their distributional range in the Bay of Bengal. An updated checklist of grunts of Bangladesh is provided.

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Intra-Task Reliability and Specificity of Individual Consistency

Perceptual and Motor Skills ◽

10.2466/pms.1970.30.2.583 ◽

1970 ◽

Vol 30 (2) ◽

pp. 583-587 ◽

Cited By ~ 7

Author(s):

Albert V. Carron

Keyword(s):

Motor Response ◽

Present Report ◽

Motor Task ◽

Response Component ◽

Linear Movement ◽

The Mean ◽

Individual Consistency ◽

Response Consistency ◽

Relationship Of ◽

The Relationship

The present report is based on reanalysis of data of Marisi (1969) in order to examine the relationship of consistency of motor response among the component responses of a single motor task. 120 high school Ss were tested on a special task, the rho. A single trial on this motor task can be logically separated into three component motor responses: reaction time, a short circular movement, and a short linear movement. The results indicated that consistency of motor response was moderately reliable within the response components but tended to be response-component specific. Further, both the reliability and specificity of motor-response consistency were independent of the size of the mean performance scores.

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DNA barcoding of bats (Chiroptera) from the Colombian northern region

Mammalia ◽

10.1515/mammalia-2020-0138 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Álvaro J. Benítez ◽

Dina Ricardo-Caldera ◽

María Atencia-Pineda ◽

Jesús Ballesteros-Correa ◽

Julio Chacón-Pacheco ◽

...

Keyword(s):

Dna Barcoding ◽

Species Identification ◽

Dna Sequences ◽

Genetic Distances ◽

Northern Region ◽

Coi Gene ◽

Individual Species ◽

Species Variation ◽

Molossus Molossus ◽

Artibeus Lituratus

Abstract Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.

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Relationship of Spiritual well-being and emotional intelligence among Iranian' nursing students

10.53350/pjmhs211561634 ◽

2021 ◽

Vol 15 (6) ◽

pp. 1634-1640

Author(s):

Javad Jafari ◽

Asra Nassehi ◽

Mohammadali Zareez ◽

Seydamalek Dadkhah ◽

Najmeh Saberi ◽

...

Keyword(s):

Emotional Intelligence ◽

Nursing Students ◽

Pearson Correlation ◽

Well Being ◽

Self Awareness ◽

Spiritual Well Being ◽

The Mean ◽

High Level ◽

Relationship Of ◽

Religious Wellbeing

Background: Among all aspects of nursing care, the spiritual one is the issue that has received little attention. Having spiritual wellbeing (SWB) is a necessity to provide appropriate spiritual care. In addition to, the Emotional intelligence (EI) is one of the most important factors in social and professional success and is essential for effective nursing practice. Therefore, aim of study was evaluating the Relationship between SWB and EI among nursing students. Methods: The sample of this descriptive-analytic study consisted of 136 nursing students studying at Bam University of Medical Sciences selected by convenience sampling method. The Bradberry and Greaves 28-item EI scale, Palutzian and Ellison SWB Scale were used to assess the total score of EI and SWB. Collected data were analyzed using descriptive statistics (mean and standard deviation), Pearson correlation coefficient, independent t-test and one-way ANOVA with SPSS v18. Results: The mean score of SWB and EI were 97.1±11.56 and 123.4 + 123.6, respectively. The mean score dimensions of SWB include (religious wellbeing 47.9±6.6, existential wellbeing 49.1±5.7) and dimensions EI: self-awareness, self-management, social awareness, and relationship management were 27.2 3 3.2, 36.2 2 5.4, 25.1 + 3.5 and 35.1 + 4.5, respectively. The majority of students have reported moderate level SWB and high level of emotional intelligence. The factors influencing their level of SWB were academic semester and age (p<0.05). Conclusion: Although the level of students' EI and SWB were at a desirable level in this study, due to the nature of nursing and the interaction between nurses and patients, providing a suitable learning environment for the development of EI is essential. Therefore, it is suggested that nursing policymakers should develop appropriate educational programs for nurses and provide curriculum for students to promote their knowledge and skills. Keywords: spiritual, religious, wellbeing, existential, nursing, emotional intelligence

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Association of Hemoglobin A1C With TDP-43 Pathology in Community-Based Elders

Neurology ◽

10.1212/wnl.0000000000012025 ◽

2021 ◽

pp. 10.1212/WNL.0000000000012025

Author(s):

Shahram Oveisgharan ◽

Ana W. Capuano ◽

Sukriti Nag ◽

Sonal Agrawal ◽

Lisa L. Barnes ◽

...

Keyword(s):

Severity Score ◽

Hemoglobin A1c ◽

Oldest Old ◽

Brain Regions ◽

Inverse Association ◽

Community Based ◽

Cytoplasmic Inclusions ◽

The Mean ◽

High Level ◽

Relationship Of

Objective.We tested the hypothesis that an inverse association exists between diabetes mellitus (DM) and hemoglobin A1C (A1C) with Transactive response DNA binding protein 43 (TDP-43) levels in older adults.Methods.We leveraged antemortem and postmortem data of decedents from three community-based clinical-pathological studies. DM status, A1C levels, and medications for DM were documented annually. TDP-43 cytoplasmic inclusions, evaluated in 6 brain regions using immunohistochemistry, were used to obtain a semiquantitative TDP-43 score (0-5) in each region, and scores were averaged across regions to obtain a TDP-43 severity score. We used linear regressions to test the association of DM and A1C with the TDP-43 severity score.Results.On average, participants (n=817) were 90 years old at the time of death, three fourth were women, and one fourth had DM. The mean A1C was 6.0% (SD=0.6). TDP-43 was observed in 54% of participants, and the mean TDP-43 score was 0.7 (range 0-4.5). A higher level of A1C was associated with a lower TDP-43 score (estimate=-0.156, S.E.=0.060, p=0.009) while DM had a borderline inverse association with the TDP-43 score (estimate=-0.163, S.E.=0.087, p=0.060). The association of higher levels of A1C with lower TDP-43 scores persisted after further adjustment by Apolipoprotein ε4, vascular risk factors, stroke, and hypoglycemic medications. Exclusion of the oldest old participants did not change the results.Conclusion.Overall, the results suggest that a high level of A1C is associated with less TDP-43 proteinopathy in older persons while the relationship of DM with TDP-43 needs further study.

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