scholarly journals Short Communication: A new primer set in CHD1 gene for bird sex identification

2021 ◽  
Vol 22 (11) ◽  
Author(s):  
Febriyanti Vera ◽  
WORAWIDH WAJJWALKU ◽  
PRAMANA YUDA ◽  
BUDI SETIADI DARYONO
Keyword(s):  
Short Communication ◽  
Natural Habitat ◽  
Bird Species ◽  
Sex Identification ◽  
Ex Situ ◽  
Universal Primers ◽  
Base Pairs ◽  
Universal Primer ◽  
Multiple Species ◽  
Ratite Birds

Abstract. Vera F, Wajjwalku W, Yuda P, Daryono BS. 2021. Short Communication: A new primer set in CHD1 gene for bird sex identification. Biodiversitas 22: 4977-4982. Determine sex is difficult for many bird species that are sexually monomorphic or only dimorphic in the adult stage. Many molecular markers have been developed for DNA sexing, which were mostly based on identifying Z and W chromosomes of avians. The sex determination of birds was mostly applied universal primer set such as P2/P8 or 2550F/2718R. However, those universal primers that were designed sometimes could not good result consistency in non-ratite birds or ratite birds. Therefore, we improved a specific primer design with deletion site in W chromosome to amplify the female-specific segments on Chromodomain-helicase DNA binding protein-1 (CHD1) gene from alignment sequences CHD1-Z and CHD1-W of Macrocephalon maleo S. Müller, 1846. This study aims to design a new pair of primer targeting a section of the CHD1 gene that can be amplified in non-ratite birds, the name of a new primer is In-Sex F/In-Sex R. A new primer set amplified DNA fragments in around 650 or 550 base pairs of CHD1-Z and also, 350 base pairs of CHD1-W. The result has successfully amplified the sex of multiple species on orders Galliformes, Passeriformes, Accipitriformes, and Strigiformes. This analysis can be helpful to the effort of in-situ or ex-situ management and conservation programs e.g the mating system in birds. And also, the analysis can be helpful for sexing data in the case of captive birds before releasing in natural habitat or reintroduction programs.

JENIS BURUNG DI KAMPUS UNIVERSITAS TANJUNGPURA

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Sutarto Kusuma Indra ◽  
Kustiati Kustiati ◽  
Rafdinal Rafdinal
Keyword(s):  
Habitat Loss ◽  
Human Life ◽  
Natural Habitat ◽  
Bird Species ◽  
Residential Land ◽  
Encounter Rates ◽  
Passer Montanus ◽  
Quality Degradation

Quality degradation, modification, and habitat loss are significant threats to bird species. The natural habitat of birds has been modified into residential land and facilities to meet the needs of human life as happened at Tanjungpura University. This study aims to determine of birds species at Tanjungpura University. Observations were carried out from January to March 2019. The method used in collecting the data from bird was “Encounter rates” which was conducted in the morning starting at 6 – 9 am and at 3 - 6 pm. The data obtained were analyzed with the formula of simple abundance scale and frequency of attendance. The birds found at Universitas Tanjungpura are 28 species classified into 23 genera, 17 families, and seven orders. Birds found to have an abundance order scale are classified into abundant, general, frequent and, unusual categories. Birds included in the abundant category are Collocalia fuciphaga and Passer montanus. The types of bird foods at Tanjungpura University consist of frugivore, insectivore, granivore, herbivore, carnivore, piscivore, omnivore, molluscivore, and nectarivore. The value of attendance frequency have range between 10-100%. The bird species with highest frequency of attendance’s value is Passer montanus, Pycnonotus aurigaster, Pycnonotus goiavier, Collocalia fuciphaga, and Anthreptes malacensis.

scholarly journals Specific Detection of Fasciola hepatica and F. gigantica in Infected Domesticated Animals Using High-Resolution Melting Analysis (HRM)

2020 ◽  
Author(s):  
Zeinab MOGHADAMIZAD ◽  
Ahmad HOSSEINI-SAFA ◽  
Mehdi MOHEBALI ◽  
Peyman HEYDARIAN ◽  
Mojgan ARYAEIPOUR ◽  
...  
Keyword(s):  
High Resolution ◽  
High Resolution Melting ◽  
Fasciola Hepatica ◽  
High Resolution Melting Analysis ◽  
Universal Primers ◽  
Specific Primer ◽  
Universal Primer ◽  
Melting Analysis ◽  
Liver Flukes ◽  
Fasciola Spp

Background: It is difficult to make an exact morphological distinction between Fasciola hepatica and Fasciola gigantica. We used High Resolution Melting analysis (HRM) method to differentiate the F. hepatica species from F. gigantica in order to differentiate them. Methods: Overall, 80 adult liver flukes were collected from infected slaughtered animals including cattle, sheep and goats from Lorestan Province, western Iran from Sep 2015 to Aug 2017. Genomic DNA was extracted using commercial DNA extraction kit. The multilocus sequences of mDNA including COX1, COX3 and ND6 were amplified employing real-time PCR & HRM analysis. Specific and universal primer pairs were designed for differentiation Fasciola spp. Results: Universal primers cannot be used to distinguish between these two species, but in the contrary, specific primer pairs of each species could differentiate them properly. Molecular identification using specific primer pairs were consistent. Conclusion: HRM is a simple, fast and reliable method for detecting and differentiating F. hepatica from F. gigantica and can be used for diagnostic and epidemiological purposes.

scholarly journals First report of Coleus blumei viroid 1 in commercial Coleus blumei in the United States

Plant Disease ◽  
2021 ◽  
Author(s):  
Gardenia Orellana ◽  
Alexander V Karasev
Keyword(s):  
United States ◽  
Leaf Tissue ◽  
The United States ◽  
Universal Primers ◽  
Rt Pcr ◽  
Universal Primer ◽  
Tissue Samples ◽  
First Report ◽  
Specific Pcr ◽  
Coleus Blumei

Coleus scutellarioides (syn. Coleus blumei) is a widely grown evergreen ornamental plant valued for its highly decorative variegated leaves. Six viroids, named Coleus blumei viroid 1 to 6 (CbVd-1 to -6) have been identified in coleus plants in many countries of the world (Nie and Singh 2017), including Canada (Smith et al. 2018). However there have been no reports of Coleus blumei viroids occurring in the U.S.A. (Nie and Singh 2017). In April 2021, leaf tissue samples from 27 cultivars of C. blumei, one plant of each, were submitted to the University of Idaho laboratory from a commercial nursery located in Oregon to screen for the presence of viroids. The sampled plants were selected randomly and no symptoms were apparent in any of the samples. Total nucleic acids were extracted from each sample (Dellaporta et al. 1983) and used in reverse-transcription (RT)-PCR tests (Jiang et al. 2011) for the CbVd-1 and CbVd-5 with the universal primer pair CbVds-P1/P2, which amplifies the complete genome of all members in the genus Coleviroid (Jiang et al. 2011), and two additional primer pairs, CbVd1-F1/R1 and CbVd5-F1/R1, specific for CbVd-1 and CbVd-5, respectively (Smith et al. 2018). Five C. blumei plants (cvs Fire Mountain, Lovebird, Smokey Rose, Marrakesh, and Nutmeg) were positive for a coleviroid based on the observation of the single 250-nt band in the RT-PCR test with CbVds-P1/P2 primers. Two of these CbVd-1 positive plants (cvs Lovebird and Nutmeg) were also positive for CbVd-1 based on the presence of a single 150-nt band in the RT-PCR assay with CbVd1-F1/R1 primers. One plant (cv Jigsaw) was positive for CbVd-1, i.e. showing the 150-nt band in RT-PCR with CbVd1-F1/R1 primers, but did not show the ca. 250-bp band in RT-PCR with primers CbVds-P1/P2. None of the tested plants were positive for CbVd-5, either with the specific, or universal primers. All coleviroid- and CbVd-1-specific PCR products were sequenced directly using the Sanger methodology, and revealed whole genomes for five isolates of CbVd-1 from Oregon, U.S.A. The genomes of the five CbVd-1 isolates displayed 96.9-100% identity among each other and 96.0-100% identity to the CbVd-1 sequences available in GenBank. Because the sequences from cvs Lovebird, Marrakesh, and Nutmeg, were found 100% identical, one sequence was deposited in GenBank (MZ326145). Two other sequences, from cvs Fire Mountain and Smokey Rose, were deposited in the GenBank under accession numbers MZ326144 and MZ326146, respectively. To the best of our knowledge, this is the first report of CbVd-1 in the United States.

An Account of Fruit and Seed Morphology, Germination and Seedling growth of Four Species of Salacia L

2019 ◽  
Vol 26 (3) ◽  
pp. 145-150
Author(s):  
Chitra Chandrasenan Rajeswary ◽  
◽  
S. Bindu ◽  
S.M. Shareef ◽  
V.S. Hima ◽  
...  
Keyword(s):  
Ex Situ Conservation ◽  
Natural Habitat ◽  
Seed Morphology ◽  
Juvenile Stage ◽  
Ex Situ ◽  
Seedling Vigour ◽  
Critical Moisture ◽  
Salacia Oblonga ◽  
Seedling Characters ◽  
Propagation Material

Seeds are the most effective and thriving propagation material of Salacia. As part of ex-situ conservation programme, four highly sought Salacia species, viz., Salacia brunoniana Wight & Arn., Salacia fruticosa Wall. Salacia malabarica Gamble and Salacia oblonga Wall. through fruit, seed and seedling characterization was carried out. For this, phenology and morphology of fruits and seeds with reference to polymorphism were documented. Effect of fresh and desiccated moisture content especially that of critical moisture were tested to understand the extent of viability of seeds. Since, these species became threatened in their natural habitat; attempts were made to standardize their seed germination characters and seedlings were raised. Seedling characters along with seedling vigour were documented up to 6 leaf stage and also an identification key was made based on their seedling characters which would aid in the demarcation of the species at their juvenile stage.

scholarly journals 454-Pyrosequencing Analysis of Bacterial Communities from Autotrophic Nitrogen Removal Bioreactors Utilizing Universal Primers: Effect of Annealing Temperature

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Alejandro Gonzalez-Martinez ◽  
Alejandro Rodriguez-Sanchez ◽  
Belén Rodelas ◽  
Ben A. Abbas ◽  
Maria Victoria Martinez-Toledo ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Nitrogen Removal ◽  
Annealing Temperature ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Universal Primers ◽  
Anammox Bacteria ◽  
Universal Primer ◽  
Optimum Annealing Temperature ◽  
Autotrophic Nitrogen Removal

Identification of anaerobic ammonium oxidizing (anammox) bacteria by molecular tools aimed at the evaluation of bacterial diversity in autotrophic nitrogen removal systems is limited by the difficulty to design universal primers for theBacteriadomain able to amplify the anammox 16S rRNA genes. A metagenomic analysis (pyrosequencing) of total bacterial diversity including anammox population in five autotrophic nitrogen removal technologies, two bench-scale models (MBR and Low Temperature CANON) and three full-scale bioreactors (anammox, CANON, and DEMON), was successfully carried out by optimization of primer selection and PCR conditions (annealing temperature). The universal primer 530F was identified as the best candidate for total bacteria and anammox bacteria diversity coverage. Salt-adjusted optimum annealing temperature of primer 530F was calculated (47°C) and hence a range of annealing temperatures of 44–49°C was tested. Pyrosequencing data showed that annealing temperature of 45°C yielded the best results in terms of species richness and diversity for all bioreactors analyzed.

scholarly journals Comparison of Two Suspension Arrays for Simultaneous Detection of Five Biothreat Bacterial in Powder Samples

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Yu Yang ◽  
Jing Wang ◽  
Haiyan Wen ◽  
Hengchuan Liu
Keyword(s):  
Bacillus Anthracis ◽  
Yersinia Pestis ◽  
Simultaneous Detection ◽  
Universal Primers ◽  
Universal Primer ◽  
Suspension Array ◽  
Specific Pathogen ◽  
Powder Samples ◽  
High Conservation ◽  
Species Specific

We have developed novel Bio-Plex assays for simultaneous detection ofBacillus anthracis, Yersinia pestis, Brucella spp., Francisella tularensis,andBurkholderia pseudomallei. Universal primers were used to amplify highly conserved region located within the 16S rRNA amplicon, followed by hybridized to pathogen-specific probes for identification of these five organisms. The other assay is based on multiplex PCR to simultaneously amplify five species-specific pathogen identification-targeted regions unique to individual pathogen. Both of the two arrays are validated to be flexible and sensitive for simultaneous detection of bioterrorism bacteria. However, universal primer PCR-based array could not identifyBacillus anthracis, Yersinia pestis,andBrucella spp.at the species level because of the high conservation of 16S rDNA of the same genus. The two suspension arrays can be utilized to detectBacillus anthracissterne spore andYersinia pestisEV76 from mimic “write powder” samples, they also proved that the suspension array system will be valuable tools for diagnosis of bacterial biothreat agents in environmental samples.

scholarly journals In situ conservation of fruit landraces

2010 ◽  
Vol 46 (Special Issue) ◽  
pp. S57-S59 ◽  
Author(s):  
F. Paprštein ◽  
J. Sedlák ◽  
V. Holubec
Keyword(s):  
Global Positioning System ◽  
Natural Habitat ◽  
In Situ Conservation ◽  
Sour Cherry ◽  
Ex Situ ◽  
The Czech Republic ◽  
Fruit Species ◽  
Global Positioning ◽  
Berry Fruits

<I>In situ </I>conservation is considered as conservation of wild biota in the natural habitat (locality). The authors extend the term to cultivated fruit species naturalised in the landscape, such as occasional spontaneous seedlings, and planted material such as old solitary trees among fields, old groves, avenues (country lanes), wind-breaks, and abandoned remnants of orchards. <I>In situ </I>conservation is also used to mark unique materials during collecting expeditions, before they will be taken as <I>ex situ </I>or proclaimed as permanent <I>in situ</I>. Important landraces found within 12 regions of the Czech Republic were registered, evaluated, and <I>in situ </I>localised by Global Positioning System (GPS). The following accessions were marked for in-situ conservation: apple (401), sweet cherry (263), pear (91), plum (42), sour cherry (27), and berry fruits (18).

scholarly journals A PCR Method That Can Be Further Developed into PCR-RFLP Assay for Eight Animal Species Identification

2018 ◽  
Vol 2018 ◽  
pp. 1-6 ◽  
Author(s):  
Feng Guan ◽  
Yu-Ting Jin ◽  
Jin Zhao ◽  
Ai-Chun Xu ◽  
Yuan-Yuan Luo
Keyword(s):  
Species Identification ◽  
Animal Species ◽  
Limit Of Detection ◽  
Cost Effective ◽  
Universal Primers ◽  
Universal Primer ◽  
Routine Identification ◽  
Pcr Rflp ◽  
Fast Processing ◽  
Rflp Assay

There are many PCR-based methods for animal species identification; however, their detection numbers are limited or could not identify unknown species. We set out to solve this problem by developing a universal primer PCR assay for simultaneous identification of eight animal species, including goat, sheep, deer, buffalo, cattle, yak, pig, and camel. In this assay, the variable lengths of mitochondrial DNA were amplified using a pair of universal primers. PCR amplifications yielded 760 bp, 737 bp, 537 bp, 486 bp, 481 bp, 464 bp, 429 bp, and 359 bp length fragments for goat, sheep, deer, buffalo, cattle, yak, pig, and camel, respectively. This primer pair had no cross-reaction with other common domestic animals and fish. The limit of detection varied from 0.01 to 0.05 ng of genomic DNA for eight animal species in a 20 µl PCR mixture. Each PCR product could be further digested into fragments with variable sizes and qualitative analysis by SspI restriction enzyme. This developed PCR-RFLP assay was sufficient to distinguish all targeted species. Compared with the previous published related methods, this approach is simple, with high throughput, fast processing rates, and more cost-effective for routine identification of meat in foodstuffs.

scholarly journals The Itombwe Massif, Democratic Republic of Congo: biological surveys and conservation, with an emphasis on Grauer's gorilla and birds endemic to the Albertine Rift

Oryx ◽  
1999 ◽  
Vol 33 (4) ◽  
pp. 301-322 ◽  
Author(s):  
Ilambu Omari ◽  
John A. Hart ◽  
Thomas M. Butynski ◽  
N. R. Birhashirwa ◽  
Agenonga Upoki ◽  
...  
Keyword(s):  
Democratic Republic ◽  
Democratic Republic Of Congo ◽  
Natural Habitat ◽  
Bird Species ◽  
Single Specimen ◽  
Biological Surveys ◽  
Albertine Rift ◽  
Nest Sites ◽  
Traditional Authorities ◽  
Over Exploitation

AbstractIn 1996, the first major biological surveys in the Itombwe Massif in over 30 years revealed that significant areas of natural habitat and remnant faunal populations remain, but that these are subject to ongoing degradation and over-exploitation. At least 10 areas of gorilla Gorilla gorilla graueri occurrence, including eight of 17 areas identified during the first survey of the species in the massif in 1959, were found. Seventy-nine gorilla nest sites were recorded and at least 860 gorillas were estimated to occupy the massif. Fifty-six species of mammals were recorded. Itombwe supports the highest representation, of any area, of bird species endemic to the Albertine Rift highlands. Twenty-two of these species were recorded during the surveys, including the Congo bay owl Phodilus prigoginei, which was previously known from a single specimen collected in Itombwe nearly 50 years ago. No part of Itombwe is officially protected and conservation initiatives are needed urgently. Given the remoteness and continuing political instability of the region, conservation initiatives must collaborate with traditional authorities based in the massif, and should focus at the outset on protecting the gorillas and limiting further degradation of key areas.

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