The phylogenetic analysis of Dalbergia (Fabaceae: Papilionaceae) based on different DNA barcodes

Holzforschung ◽  
2017 ◽  
Vol 71 (12) ◽  
pp. 939-949 ◽  
Author(s):  
Qiwei Li ◽  
Jihong Wu ◽  
Yesheng Wang ◽  
Xiaoming Lian ◽  
Feilong Wu ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Reliable Method ◽  
Dna Barcodes ◽  
Illegal Logging ◽  
Good Discrimination ◽  
Close Match ◽  
Discrimination Ability ◽  
Overall Performance ◽  
Resources Conservation ◽  
Barcode Gap

AbstractThe genusDalbergiacontains approximately 250 species with many valuable trees being destroyed by targeted and illegal logging. DNA barcoding is a reliable method for the molecular identification of different species and resources conservation. In the present study, the specimen discrimination ability of internal transcribed spacer (ITS),matK,rbcL andpsbA-trnH barcoding were tested onDalbergiasequences, downloaded from the National Center for Biotechnology Information (NCBI), and the combined barcoding ITS+matK+rbcL was used to identify unknown specimens. It was found that ITS+matK+rbcL have good discrimination rates based on the analysis methods best match (BM) and best close match (BCM). These barcodes also have the best performance concerning barcode gap distribution, and are able to discriminate unknown specimens from South-China. Furthermore, it was demonstrated thatD. tamarindifoliaandD. rubiginosaare also relatively close to sister-speciesD. pinnataandD. candenatensiswithin the phylogeneticDalbergiatree. Considering the overall performance of these barcodes, we suggest that the ITS+matK+rbcL region is a suitable barcode for identifyingDalbergiaspecies.

Phylogenetic analysis of Aquilaria Lam. (Thymelaeaceae) based on DNA barcoding

Holzforschung ◽  
2019 ◽  
Vol 73 (6) ◽  
pp. 517-523 ◽  
Author(s):  
Tingting Feng ◽  
Qiwei Li ◽  
Yesheng Wang ◽  
Simin Qiu ◽  
Mengling He ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationship ◽  
Genetic Distances ◽  
Ribulose Bisphosphate Carboxylase ◽  
Good Discrimination ◽  
Bisphosphate Carboxylase ◽  
Close Match ◽  
Discrimination Ability ◽  
Illegal Harvesting ◽  
Overall Performance

AbstractAquilariaLam. is an important group of trees that produce agarwood, which is widely used for manufacturing medicine, perfumes and incense. The members of the genusAquilariaare close to being extinct due to illegal harvesting and are now protected in many countries. In this study, five DNA barcodes [internal transcribed spacer (ITS), maturase K (matK),psbA-trnH, ribulose bisphosphate carboxylase (rbcL) andtrnL-trnF] and their combinations were evaluated for the discrimination of the major (16 out of 21) species ofAquilariabased on three criteria: sequence variation, genetic distances and the discrimination ability. In addition, we attempted to determine the phylogenetic relationship betweenAquilariaandGyrinopsspecies using three phylogenetic analysis methods. We observed that the combination barcode ITS+trnL-trnF had a good discrimination ability based on the best match and best close match methods, provided more genetic information, and clearly indicated the comprehensive phylogenetic relationship between mostAquilariaandGyrinopsspecies. Considering the overall performance of these barcodes, the ITS+trnL-trnF is a suitable barcode for the identification ofAquilariaspecies.

scholarly journals Two New Records of Upeneus Spottocaudalis and U. Sundaicus (Perciformes: Mullidae) from the Northern South China Sea Based on the Morphology and DNA Barcoding

2021 ◽  
Author(s):  
Zhisen Luo ◽  
Murong Yi ◽  
Kangwen Qiu ◽  
Sibiao Liu ◽  
Sui Gu ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
New Records ◽  
Northern South China Sea ◽  
Genetic Distances ◽  
Dna Barcodes ◽  
China Sea ◽  
Homologous Sequences ◽  
Nj Tree ◽  
Barcode Gap

Abstract In this study, two new records of goatfishes Upeneus spottocaudalis and U. sundaicus from the South China Sea, combing evidence from morphology and DNA barcodes for species identification. ML tree and NJ tree result showed that the sequences of U. spottocaudalis and U. sundaicus were clustered with the homologous sequences form GenBank, respectively, and the intraspecific genetic distances of U. spottocaudalis (0.2%) and U. sundaicus (0.3%) were less than 2%. Automatic Barcode Gap Discovery (ABGD) analysis also supported this result of classification.

scholarly journals Nomogram to predict overall survival for patients with pseudomyxoma peritonei of appendiceal origin: A retrospective cohort study

2020 ◽  
Author(s):  
Mingjian Bai ◽  
Shilong Wang ◽  
Ruiqing Ma ◽  
Ying Cai ◽  
Yiyan Lu ◽  
...  
Keyword(s):  
Overall Survival ◽  
Pseudomyxoma Peritonei ◽  
Roc Analysis ◽  
Prediction Models ◽  
Radical Surgery ◽  
Individual Risk ◽  
Good Discrimination ◽  
Internal Validation ◽  
Discrimination Ability ◽  
First Time

Abstract Background Pseudomyxoma peritonei (PMP) is a rare disease, the prognosis of overall survival (OS) is affected by many factors, present study aim to define independent prediction indicators and establish a nomogram for PMP patients.Methods 119 PMP patients received cytoreductive surgery (CRS) combined with hyperthermic intraperitoneal chemotherapy (HIPEC) in our center for the first time were included between 01/06/2013 and 22/11/2019 . The log-rank test was used to compare the OS rate among groups, subsequently, variables with P<0.10 were subjected to multivariate Cox model for defining independent prediction indicators. Finally, the nomogram prediction models will be established and for internal validation.Results Multivariate analysis showed Sex, D-Dimer, CA125, CA19-9, PCI, and degree of radical surgery were independently associated with OS in PMP patients. A nomogram was plotted based on the independent predictive factors and undergone internal validation, ROC analysis was performed to calculate discrimination ability of the nomogram, the C-index was 0.880 (95%CI: 0.806- 0.933) and calibration plots showed good performance. Conclusions Six independent prognostic factor for predicting survival in PMP patients were difined, the nomogram has a good discrimination ability for individual risk predition, more researches are needed to verify and improve the prediction model.

scholarly journals Species delimitation and life stage association of Propsilocerus Kieffer, 1923 (Diptera, Chironomidae) using DNA barcodes

ZooKeys ◽  
2020 ◽  
Vol 975 ◽  
pp. 79-86
Author(s):  
Hai-Jun Yu ◽  
Xiao-Long Lin ◽  
Rui-Lei Zhang ◽  
Qian Wang ◽  
Xin-Hua Wang
Keyword(s):  
Species Delimitation ◽  
Life Stage ◽  
Dna Barcodes ◽  
Neighbor Joining ◽  
Index Numbers ◽  
Nj Tree ◽  
Barcode Gap

The utility of COI DNA barcodes in species delimitation is explored as well as life stage associations of five closely related Propsilocerus species: Propsilocerus akamusi (Tokunaga, 1938), Propsilocerus paradoxus (Lundström, 1915), Propsilocerus saetheri Wang, Liu et Paasivirta, 2007, Propsilocerus sinicus Sæther et Wang, 1996, and Propsilocerus taihuensis (Wen, Zhou et Rong, 1994). Results revealed distinctly larger interspecific than intraspecific divergences and indicated a clear “barcode gap”. In total, 42 COI barcode sequences including 16 newly generated DNA barcodes were applied to seven Barcode Index Numbers (BINs). A neighbor-joining (NJ) tree comprises five well-separated clusters representing five morphospecies. Comments on how to distinguish the larvae of P. akamusi and P. taihuensis are provided.

The Low Copy Nuclear Gene Region, Granule Bound Starch Synthase (GBSS1), as a Novel Mini-DNA Barcode for the Identification of Different Sage (Salvia) Species

Planta Medica ◽  
2021 ◽  
Author(s):  
Iffat Parveen ◽  
Natascha Techen ◽  
Sara M. Handy ◽  
Jing Li ◽  
Charles Wu ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Dna Barcode ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Starch Synthase ◽  
Species Discrimination ◽  
Success Rates ◽  
Discrimination Ability ◽  
Internal Transcribed Spacer 2 ◽  
Granule Bound Starch Synthase

AbstractMorphological similarity within species makes the identification and authentication of Salvia species challenging, especially in dietary supplements that contain processed root or leaf powder of different sage species. In the present study, the species discriminatory power of 2 potential DNA barcode regions from the nuclear genome was evaluated in 7 medicinally important Salvia species from the family Lamiaceae. The nuclear internal transcribed spacer 2 and the exon 9 – 14 region of low copy nuclear gene WAXY coding for granule-bound starch synthase 1 were tested for their species discrimination ability using distance, phylogenetic, and BLAST-based methods. A novel 2-step PCR method with 2 different annealing temperatures was developed to achieve maximum amplification from genomic DNA. The granule-bound starch synthase 1 region showed higher amplification and sequencing success rates, higher interspecific distances, and a perfect barcode gap for the tested species compared to the nuclear internal transcribed spacer 2. Hence, these novel mini-barcodes generated from low copy nuclear gene regions (granule-bound starch synthase) that were proven to be effective barcodes for identifying 7 Salvia species have potential for identification and authentication of other Salvia species.

Manganese(II)-ion-selective electrode based on 2,2′-bis(salicylideneamino)azobenzene incorporated in poly(vinyl chloride) matrix

2009 ◽  
Vol 74 (9) ◽  
pp. 1411-1424 ◽  
Author(s):  
Mohammad Bagher Gholivand ◽  
Maryam Gorji ◽  
Mohammad Joshaghani
Keyword(s):  
Pvc Membrane ◽  
Indicator Electrode ◽  
Membrane Electrode ◽  
Selective Electrode ◽  
Good Discrimination ◽  
Discrimination Ability ◽  
Poly Vinyl Chloride ◽  
Pvc Membrane Electrode ◽  
Chloride Matrix

A new PVC membrane electrode highly selective to Mn(II), based on 2,2′-bis(salicylideneamino)azobenzene as an ionophore. The electrode exhibits a Nernstian response to Mn(II) ions over a concentration range 0.8 × 10–1–1.1 × 10–7 mol l–1 with a slope of 30.5 ± 0.5 mV per decade and detection limit 5.5 × 10–8 mol l–1. The electrode was used for 45 days at the minimum without any measurable potential divergence. Also, the electrode revealed a fairly good discrimination ability between Mn(II) ions and some cations and anions. The electrode was also utilized as indicator electrode in the potentiometric titration of Mn(II) with EDTA and in determination of Mn(II) in drug as well as tape and river water.

scholarly journals DNA barcodes identify medically important tick species in Canada

Genome ◽  
2017 ◽  
Vol 60 (1) ◽  
pp. 74-84 ◽  
Author(s):  
Danielle A. Ondrejicka ◽  
Kevin C. Morey ◽  
Robert H. Hanner
Keyword(s):  
Dna Barcode ◽  
Nearest Neighbour ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Genetic Cluster ◽  
Potential Health ◽  
Intraspecific Divergence ◽  
Coi Sequences ◽  
I Gene ◽  
Barcode Gap

Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5′ region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species. The tree topology was further supported by a BIN analysis. COI sequences generated were found to have a mean maximum intraspecific divergence of 1.59% and a mean nearest neighbour divergence of 12.8%, indicating a significant “barcode gap”. This study also revealed possible cryptic diversity among specimens morphologically identified as Ixodes soricis and Ixodes texanus. A PCR-based test for Borrelia burgdorferi determined that 18.1% of Lyme-competent ticks in this study were positive. This study is also the first to record a B. burgdorferi-positive exoskeleton. In conclusion, DNA barcoding is a powerful tool that clinicians can use to determine the identification of tick specimens which can help them to suggest whether an attached tick is a potential health risk.

MEASUREMENTS AND CHARACTERIZATIONS OF MECHANICAL PROPERTIES OF HUMAN SKINS

2013 ◽  
Vol 24 ◽  
pp. 1360029
Author(s):  
HAN WOOK SONG ◽  
YON KYU PARK
Keyword(s):  
Mechanical Properties ◽  
Alternative Medicine ◽  
Elastic Coefficient ◽  
Good Discrimination ◽  
Discrimination Ability ◽  
Repeatability Error ◽  
Skin Physiology ◽  
Decompression Tube ◽  
External Stimuli

A skin is an indispensible organ for humans because it contributes to metabolism using its own biochemical functions and protects the human body from external stimuli. Recently, mechanical properties such as a thickness, a friction and an elastic coefficient have been used as a decision index in the skin physiology and in the skin care market due to the increased awareness of wellbeing issues. In addition, the use of mechanical properties is known to have good discrimination ability in the classification of human constitutions, which are used in the field of an alternative medicine. In this study, a system that measures mechanical properties such as a friction and an elastic coefficient is designed. The equipment consists of a load cell type (manufactured by the authors) for the measurements of a friction coefficient, a decompression tube for the measurement of an elastic coefficient. Using the proposed system, the mechanical properties of human skins from different constitutions were compared, and the relative repeatability error for measurements of mechanical properties was determined to be less than 2%. Combining the inspection results of medical doctors in the field of an alternative medicine, we could conclude that the proposed system might be applicable to a quantitative constitutional diagnosis between human constitutions within an acceptable level of uncertainty.

scholarly journals The development and assessment of a bacteriocin typing method forKlebsiella

1979 ◽  
Vol 82 (2) ◽  
pp. 207-223 ◽  
Author(s):  
A. S. Edmondson ◽  
E. Mary Cooke
Keyword(s):  
Close Agreement ◽  
Reliable Method ◽  
Natural Populations ◽  
Good Discrimination ◽  
Typing Method ◽  
Acceptable Accuracy ◽  
Cultural Conditions ◽  
Typing Methods ◽  
Complete Set ◽  
Bacteriocin Typing

SUMMARYKlebsiellas are generally typed by the method of capsular serotyping but, although this is a reliable method, it is time consuming, requires the production of a large number of antisera and is not generally available. For this reason another method for typing klebsiellas was sought.A bacteriocin typing method involving mitomycin C induction was developed and the cultural conditions giving optimum klebecin production and the best methods of testing the sensitivity of the organisms to klebecins were determined.Of 190 klebsiella strains screened for bacteriocinogeny, only 68 (35·8%) produced klebecin and after calculation of similarity values by computer analysis, a typing set of 15 producers was selected. This typing set allowed over 96% of klebsiella strains to be typed and tests of the reproducibility of the method and the variability of typing patterns in natural populations of klebsiella indicated that results of acceptable accuracy could be obtained, while retaining good discrimination if two or more differences were required between patterns before they were regarded as distinct.A complete set of capsular antisera were prepared, enabling the results obtained from klebecin typing to be compared with those from serotyping. There was generally close agreement between the results from the two typing methods and greater discrimination was obtained between similar strains when the two methods were combined. Klebecin typing and serotyping revealed relationships between strains from five outbreaks of infection, and strains of the same serotype from different hospitals could frequently be distinguished by their klebecin typing patterns.

scholarly journals Identification of species and materia medica withinSaussureasubg.Amphilaenabased on DNA barcodes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6357 ◽  
Author(s):  
Jie Chen ◽  
Yong-Bao Zhao ◽  
Yu-Jin Wang ◽  
Xiao-Gang Li
Keyword(s):  
Internal Transcribed Spacer ◽  
Evolutionary History ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Additional Species ◽  
Plant Materials ◽  
Materia Medica ◽  
The Family ◽  
Identification Of Species ◽  
Medical Plants

Saussureais one of the most species-rich genera in the family Asteraceae, where some have a complex evolutionary history, including radiation and convergent evolution, and the identification of these species is notoriously difficult. This genus contains many plants with medical uses, and thus an objective identification method is urgently needed.Saussureasubg.Amphilaenais one of the four subgenera ofSaussureaand it is particularly rich in medical resources, where 15/39 species are used in medicine. To test the application of DNA barcodes in this subgenus, five candidates were sequenced and analyzed using 131 individuals representing 15 medical plants and four additional species from this subgenus. Our results suggested that internal transcribed spacer (ITS) +rbcL or ITS +rbcL +psbA-trnH could distinguish all of the species, while the ITS alone could identify all of the 15 medical plants. However, the species identification rates based on plastid barcodes were low, i.e., 0% to 36% when analyzed individually, and 63% when all four loci were combined. Thus, we recommend using ITS +rbcL as the DNA barcode forS.subg.Amphilaenaor the ITS alone for medical plants. Possible taxonomic problems and substitutes for medicinal plant materials are also discussed.

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