scholarly journals Genetic diversity and phylogenetic relationship among Anabantoidei fish (Anabantiformes) in South Kalimantan, Indonesia based on SDS-PAGE analysis

2019 ◽  
Vol 20 (9) ◽  
Author(s):  
Rani Sasmita ◽  
Mabrur Mabrur ◽  
UMMY SHALIHA AULIA RAHMY ◽  
Badruzsaufari Badruzsaufari
Keyword(s):  
Genetic Diversity ◽  
Ammonium Sulfate ◽  
Phylogenetic Relationship ◽  
Soluble Protein ◽  
Phylogenetic Trees ◽  
Protein Profile ◽  
Phylogenetic Reconstruction ◽  
Fish Muscle ◽  
Freshwater Ecosystem ◽  
Sds Page

Abstract. Sasmita R, Mabrur, Rahmy USA, Badruzsaufari. 2019. Genetic diversity and phylogenetic relationship among Anabantoidei fish (Anabantiformes) in South Kalimantan, Indonesia based on SDS-PAGE analysis. Biodiversitas 20: 2519-2527. Protein profile is a molecular marker for diversity and phylogenetic analysis of germplasm, including Anabantoidei fish which is abundant in freshwater ecosystem of South Kalimantan. The aim of this research was to analyze genetic diversity and construct phylogenetic relationship among Anabantoidei fish based on SDS PAGE analysis. Protein was extracted from muscle tissue of six species of Anabantoidei fish and precipitated using Ammonium sulfate salt. Soluble protein content was determined using Bradford assay and then separated based on SDS-PAGE method. Genetic diversity and phylogenetic relationship were constructed using PAST software based on UPGMA method. The results showed that the soluble protein of fish muscle can be precipitated optimally in different ammonium sulfate concentration. Based on SDS-PAGE analysis, 59 different protein bands have been separated from gels with molecular weight ranging from 28.15 to 181.61 kDa. On the protein level, the Anabantoidei fish showed high genetic polymorphism (greater than 90%) with 3, 2 and 5 monomorphic bands on non-precipitated, AS-precipitated and combination between non- and AS-precipitated proteins, respectively. The phylogenetic reconstruction also exhibited that the Anabantoidei fish has the unique phylogenetic trees, especially for the combined protein datasets. This information would be useful for freshwater fish conservation and breeding programs.

scholarly journals Estimation of genetic diversity in the germplasm of Brassica Campestris (L.) Using morphological and biochemical markers

2017 ◽  
pp. 45-58
Author(s):  
ZAKIR ULLAH
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Relationship ◽  
Biochemical Markers ◽  
Morphological Traits ◽  
Brassica Campestris ◽  
Morphological Characters ◽  
Research Centre ◽  
Sds Page ◽  
Plant Sciences ◽  
The Common

A total of 60 genotypes of Brassica campestris (L) germplasm were acquired from National Research Centre (NARC) Islamabad, Pakistan for the evaluation of genetic diversity using the morphological characters and SDS-PAGE analysis. These genotypes were grown-up in Plant Garden Department of plant sciences, University of Malakand, Khyber Pukhtunkhwa, Pakistan. For the assessment of genetic diversity total of 18 morphological traits were scored and their phylogenetic relationship were plot through cluster diagram. For the estimation of genetic diversity, we used the most influential technique SDS PAGE. We observed six loci (bands) from the collected genotypes; locus-1 (band-1) contained 100% bands of protein and obvious as monomorphic locus while loci i.e. 2,3,4,5 and 6 showed 28%, 42%, 36%, 56% and 25%, respectively variation and were polymorphic. The inter species locus influence toward genetic assortment (LCTGA) was 83.33% in the attained genotypes. Profiling through SDS PAGE based on two-way cluster plottingresolved effectively the collected genotype into 4 cluster. We consider that this work provides a baseline for the understanding genetic diversity in the common crops used in Pakistan and warrants further investigation in this newly evolving field of study.

scholarly journals Molecular Diversity of The Tidal Swamp Rice (Oryza sativa L.) Germplasm of The South Kalimantan, Indonesia

2018 ◽  
Author(s):  
Dindin H. Mursyidin ◽  
Purnomo Purnomo ◽  
Issirep Sumardi ◽  
Budi S. Daryono
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Intergenic Spacer ◽  
The South ◽  
Abiotic And Biotic Stresses ◽  
Intergenic Spacer Region ◽  
Biotic Stresses ◽  
Tidal Swamp ◽  
Wide Range

Tidal swamp rice has long been cultivated by the local people of the South Kalimantan, Indonesia. This germplasm possess some important traits for adapted to a wide range of abiotic and biotic stresses. In this study, a total of sixteen cultivars of this germplasm, consisting of fifteen of the South Kalimantan Province and one of Sumatera Island, Indonesia (an outgroup) were analyzed, phylogenetically based on the chloroplast trnL-F and nuclear intergenic spacer region (IGS). The results showed that this germplasm has a relatively more extraordinary genetic diversity than other local rice germplasm. In a nucleotide level, this germplasm showed a genetic diversity of 0.61 for nuclear IGS and 0.58 for trnL-F. The phylogenetic reconstruction also exhibited that this germplasm has the unique illustration of phylogenetic trees, particularly for the combined sequence datasets. Thus, the results of our study would provide useful information for further understanding of evolutionary relationships of this germplasm and facilitate the efficient utilization of valuable genes for genetic improvement, particularly in the tidal swamp areas.

scholarly journals Phylogenetically resolving epidemiologic linkage

2016 ◽  
Vol 113 (10) ◽  
pp. 2690-2695 ◽  
Author(s):  
Ethan O. Romero-Severson ◽  
Ingo Bulla ◽  
Thomas Leitner
Keyword(s):  
Sample Size ◽  
Phylogenetic Relationship ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Tree Topology ◽  
Common Source ◽  
Coalescent Model ◽  
Hiv 1 ◽  
Transmission Direction

Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals’ HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.

scholarly journals Protein Profile Study of Some Nigerian Sesame (Sesamum indicum L.) Accessions

2015 ◽  
Vol 3 (2) ◽  
pp. 322-329 ◽  
Author(s):  
Gbenga Olorunshola Alege
Keyword(s):  
Genetic Diversity ◽  
Protein Profile ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Sesamum Indicum ◽  
Genomic Changes ◽  
Sds Page ◽  
Sesame Genotypes ◽  
Species Specific ◽  
Total Seed

This study was carried out to investigate the genetic diversity among 23 sesame (Sesamum indicum L.) accessions obtained from different agro-ecological localities from 10 different states across 4 geopolitical zones in Nigeria using evidence from Sodium Dodecyl Polyacrylamide Gel Electrophoresis (SDS-PAGE). Total seed protein of the studied plants resolved on 12% SDS-PAGE showed variations in numbers and intensity of bands among the different sesame accessions. Thirteen (13) major bands were recorded in this study. Lack of unique band and presence of common band (band 7) among the 23 studied sesame accessions indicate some levels of genetic affinity and evidence of common evolutionary origin of the sesame genotypes. This band can therefore be tagged as species specific band for discriminating Sesamum indicum. Cluster analysis grouped the 23 sesame genotypes into two clusters with similarity coefficient ranging from 0.42 to 0.96 which indicates existence of genetic diversity; therefore there is ample opportunity for improving the 23 sesame genotypes. Variations in protein bands observed among the 23 studied plants could be attributed to genomic changes taken place during species diversification. It can be concluded that genetic diversity existed among Nigerian sesame for the improvement of characters of interest. Accessions 9 (YOL), 15(OTT), 22 (OFF) and 23 (JAL) are therefore recommended for used in future breeding programs for the development of improved sesame varieties.Int J Appl Sci Biotechnol, Vol 3(2): 322-329 DOI: http://dx.doi.org/10.3126/ijasbt.v3i2.12734

scholarly journals Genetic variations in Turkey cultivar and ecotype Medicago sativa species: cytological, total protein profile, and molecular characterization

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Büşra Yazıcılar ◽  
Gholamreza Jannati ◽  
Ismail Bezirganoglu
Keyword(s):  
Genetic Diversity ◽  
Flow Cytometry ◽  
Medicago Sativa ◽  
Cytogenetic Analysis ◽  
Nutritional Value ◽  
Protein Profile ◽  
Control Plant ◽  
Perennial Plant ◽  
Sds Page ◽  
Simple Sequence

Abstract Background Alfalfa(Medicago sativa L.) is a perennial plant, which is high in nutritional value and resistant to environmental conditions, and it is one of most frequently preferred feed crop among the leguminous family. In this study, it was aimed to determine the genetic diversity of some alfalfa ecotypes and their varieties by DNA, protein, nucleus, and chromosome counts. The genetic distance between the populations of control (M. truncatula), five different cultivars (Alsancak, Bilensoy, Iside, Plato, Bilensoy82), and three different ecotypes (Erzurum, Muş, and Konya) was investigated by cytogenetic analysis, flow cytometry, simple sequence repeats (SSR), and SDS PAGE techniques. Results Cytogenetic analysis of these tested plants has verified the existence of expected levels such as diploid, triploid, and tetraploid as well as aneuploid (2n = 4x = 30) plants. Flow cytometry analysis have displayed that all of tested plants were tetraploid, whereas cytological analysis had either diploid, triploid, or tetraploid. Genetic diversity dendrogram was created using Erzurum, Muş, Konya, Bilensoy82, Alsancak, and Plato varieties. The Iside and Bilensoy were found to be morphogenetic in relationship. Our control plant, M. truncatula, did not have a similarity relationship with other ecotypes and cultivars. The total numbers of protein bands differed among tested plants from 140 kDA to 25 kDa. Conclusions This paper first reports on the genetic variation of Turkish alfalfa plants by using detailed analysis techniques. This work provides important findings for the classification, conservation, and innovation of alfalfa germplasm resources.

scholarly journals The Quality of Dory Fillets based on Water Soluble Protein, Color, and Myoglobin Concentration

2016 ◽  
Vol 19 (1) ◽  
pp. 44
Author(s):  
Nurfajrin Nisa ◽  
Mala Nurilmala ◽  
Tati Nurhayati ◽  
Nurlisa Butet
Keyword(s):  
Soluble Protein ◽  
Protein Profile ◽  
Water Soluble ◽  
Color Measurement ◽  
Protein Profiles ◽  
Water Soluble Protein ◽  
Sds Page

<p>Fillet of dory is very easy to be find in Indonesian market with various brand and produsen.<br />Imported dory fillet is preferred by consumer so far because it has a white color compare than local<br />fillets. Color is the important parameter that used by consumers to determine the quality of filet. This<br />study was aimed to determine the quality of local and imported fillets, including protein profile using<br />SDS PAGE, color measurement, and myoglobin extractability. The results of water soluble protein profiles<br />showed dory fillet contained 13-15 bands. The redness value (a*) of local fillet (DN, DL, DM) was higher<br />compared others. However, imported fillet (DI) had the highest if redness index (a/b). Imported fillet (DI)<br />showed the lowest concentration of myoglobin compared other samples.</p>

scholarly journals Genetic diversity and phylogenetic relationship of higher termite Globitermes sulphureus (Haviland)(Blattodea:Termitidae)

Sociobiology ◽  
2021 ◽  
Vol 68 (2) ◽  
pp. 5911
Author(s):  
Nurul Akmar Hussin ◽  
Abdul Hafiz Ab Majid
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Relationship ◽  
Phylogenetic Trees ◽  
Haplotype Diversity ◽  
Evolutionary Genetics ◽  
Neighbor Joining ◽  
Geographic Isolation ◽  
Neutral Genetic Diversity ◽  
Coii Gene ◽  
Relationship Of

The subterranean higher termite Globitermes sulphureus (Blattodea: Termitidae), is a peridomestic forager and regarded as a significant pest in Southeast Asia. In this study, the populations of G. sulphureus from the USM main campus area were investigated based on partial sequences of the mitochondrial COII gene. The genetic diversity was determined using DnaSP v5 software while the phylogenetic relationship was defined using Neighbor-joining (NJ) and maximum likelihood (ML) methods using Molecular Evolutionary Genetics Analysis (MEGA 7) software. A total of 2 haplotypes were detected among the 5 sample sequences that differed by two variable sites. In addition, both phylogenetic trees gave similar topology and supporting the results from haplotype diversity. Based on the haplotype diversity and molecular phylogeny, it is proposed that geographic isolation and lack of human activities have contributed to the neutral genetic diversity of G. sulphureus.   

scholarly journals Profil Protein Trypanosoma evansi dari Daerah Geografis Berbeda di Indonesia Tahun 2012-2014 dengan Sodium Dodecil Sulphate Polyacrylamide Gel Electrophoresis (TRYPANOSOMA EVANSI PROTEIN PROFILE OF DIFFERENT GEOGRAPHICAL AREAS ORIGIN IN INDONESIA

2018 ◽  
Vol 18 (4) ◽  
pp. 526
Author(s):  
Fitrine Ekawasti ◽  
Ichwan Yuniarto ◽  
Sulinawati Sulinawati ◽  
Didik Tulus Subekti
Keyword(s):  
Soluble Protein ◽  
Serological Test ◽  
Protein Profile ◽  
Polyacrylamide Gel Electrophoresis ◽  
Trypanosoma Evansi ◽  
Blue Staining ◽  
Protein Profiles ◽  
Coomassie Blue Staining ◽  
Coomassie Blue ◽  
Sds Page

Surra outbreak in 2012 has led to more than 1,700 animals have died in the province of East Nusa Tenggara (NTT) Indonesia. Surra case sporadically continues throughout the year in various areas, especially Kalimantan, Banten as well as other areas. Some reports reveal differences in protein profiles among multiple isolates of T. evansi. Therefore the purpose of this research were to find out the protein profile of each isolate T. evansi in Indonesia and the possible biological differences among them. Eleven isolates originating from the province of East Nusa Tenggara, South Kalimantan and Central Kalimantan, Banten, Lampung and Bengkulu has been isolated and purified Using DEAE. Trypanosoma isolate were frezeethawing repeatedly to obtain soluble protein. Furthermore, soluble protein is treated with heating or without heating and then each was run on SDS PAGE with Coomassie Blue staining. The protein profiles of all isolates were compared each other. The results showed that eleven isolates of T. evansi in Indonesia has a very diverse protein profile. Then for the purposes of development of diagnostic kit can be used whole lysate cell (WCL) as stock antigen in serological test process.

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