scholarly journals The new Internal Transcribed Spacer 2 diagnostic tool clarifies the taxonomic position and geographic distribution of the North American malaria vector Anopheles punctipennis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
James M. Hodge ◽  
Andrey A. Yurchenko ◽  
Dmitriy A. Karagodin ◽  
Reem A. Masri ◽  
Ryan C. Smith ◽  
...  
Keyword(s):  
Malaria Vector ◽  
Internal Transcribed Spacer ◽  
Single Species ◽  
Its2 Sequence ◽  
Pathogen Transmission ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Sequence Length ◽  
Phylogenetic Position ◽  
Internal Transcribed Spacer 2

Abstract Background The malaria mosquito Anopheles punctipennis, a widely distributed species in North America, is capable of transmitting human malaria and is actively involved in the transmission of the ungulate malaria parasite Plasmodium odocoilei. However, molecular diagnostic tools based on Internal Transcribed Spacer 2 (ITS2) of ribosomal DNA are lacking for this species. Anopheles punctipennis is a former member of the Anopheles maculipennis complex but its systematic position remains unclear. Methods In this study, ITS2 sequences were obtained from 276 An. punctipennis specimens collected in the eastern and midwestern United States and a simple and robust Restriction Fragment Length Polymorphism approach for species identification was developed. The maximum-likelihood phylogenetic tree was constructed based on ITS2 sequences available through this study and from GenBank for 20 species of Anopheles. Results The analysis demonstrated a consistent ITS2 sequence length and showed no indications of intragenomic variation among the samples based on ITS2, suggesting that An. punctipennis represents a single species in the studied geographic locations. In this study, An. punctipennis was found in urban, rural, and forest settings, suggesting its potential broad role in pathogen transmission. Phylogeny based on ITS2 sequence comparison demonstrated the close relationship of this species with other members of the Maculipennis group. Conclusions This study developed molecular tools based on ITS2 sequences for the malaria vector An. punctipennis and clarified the phylogenetic position of the species within the Maculipennis group.

scholarly journals The New Internal Transcribed Spacer 2 Diagnostic Tool Clarifies the Taxonomic Position and Geographic Distribution of the North American Malaria Vector Anopheles Punctipennis

2020 ◽  
Author(s):  
James M. Hodge ◽  
Andrey A. Yurchenko ◽  
Dmitriy A. Karagodin ◽  
Reem A. Masri ◽  
Ryan C. Smith ◽  
...  
Keyword(s):  
Malaria Vector ◽  
Internal Transcribed Spacer ◽  
Single Species ◽  
Its2 Sequence ◽  
Pathogen Transmission ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Sequence Length ◽  
Phylogenetic Position ◽  
Internal Transcribed Spacer 2

Abstract Background: The malaria mosquito Anopheles punctipennis Say, a widely distributed species in North America, is capable of transmitting human malaria and is actively involved in the transmission of the ungulate malaria parasite Plasmodium odocoilei. However, molecular diagnostic tools based on Internal Transcribed Spacer 2 (ITS2) of ribosomal DNA are lacking for An. punctipennis. An. punctipennis is a former member of the Anopheles maculipennis complex but its systematic position remains unclear. Results: In this study, we collected and sequenced ITS2 from 276 An. punctipennis specimens collected from the eastern and midwestern United States. Our analysis demonstrated a consistent sequence length and showed no indications of intragenomic variation among the samples based on ITS2, suggesting that An. punctipennis represents a single species in the studied geographic locations. In addition to the ITS2 sequence-based molecular tool, we developed a simple and robust Restriction Length Polymorphism approach for species identification. An. punctipennis was found in urban, rural, and forest settings, suggesting its potential broad role in pathogen transmission. Phylogeny based on ITS2 sequence comparison demonstrated the close relationship of this species with other members of the Maculipennis group. Conclusions: This study developed molecular tools based on ITS2 sequences for the malaria vector An. punctipennis and clarified the phylogenetic position of the species within the Maculipennis group.

scholarly journals Endangered Uyghur Medicinal PlantFerulaIdentification through the Second Internal Transcribed Spacer

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Congzhao Fan ◽  
Xiaojin Li ◽  
Jun Zhu ◽  
Jingyuan Song ◽  
Hui Yao
Keyword(s):  
Medicinal Plant ◽  
Related Species ◽  
Internal Transcribed Spacer ◽  
Morphological Characteristics ◽  
Its2 Sequence ◽  
Sequence Length ◽  
Local Alignment ◽  
Accurate Identification ◽  
Distance Method ◽  
Closely Related Species

The medicinal plantFerulahas been widely used in Asian medicine, especially in Uyghur medicine in Xinjiang, China. Given that various substitutes and closely related species have similar morphological characteristics,Ferulais difficult to distinguish based on morphology alone, thereby causing confusion and threatening the safe use ofFerula. In this study, internal transcribed spacer 2 (ITS2) sequences were analyzed and assessed for the accurate identification of two salableFerulaspecies (Ferula sinkiangensisandFerula fukangensis) and eight substitutes or closely related species. Results showed that the sequence length of ITS2 ranged from 451 bp to 45 bp, whereas guanine and cytosine contents (GC) were from 53.6% to 56.2%. A total of 77 variation sites were detected, including 63 base mutations and 14 insertion/deletion mutations. The ITS2 sequence correctly identified 100% of the samples at the species level using the basic local alignment search tool 1 and nearest-distance method. Furthermore, neighbor-joining tree successfully identified the genuine plantsF. sinkiangensisandF. fukangensisfrom their succedaneum and closely related species. These results indicated that ITS2 sequence could be used as a valuable barcode to distinguish Uyghur medicineFerulafrom counterfeits and closely related species. This study may broaden DNA barcoding application in the Uyghur medicinal plant field.

Evolution and function of B chromosome 45S rDNA sequences in Brachycome dichromosomatica

Genome ◽  
2007 ◽  
Vol 50 (7) ◽  
pp. 638-644 ◽  
Author(s):  
Sylvia Marschner ◽  
Armin Meister ◽  
Frank R. Blattner ◽  
Andreas Houben
Keyword(s):  
Phylogenetic Analysis ◽  
Internal Transcribed Spacer ◽  
B Chromosome ◽  
Its2 Sequence ◽  
B Chromosomes ◽  
Rrna Gene ◽  
45S Rdna ◽  
Internal Transcribed Spacer 2 ◽  
Rdna Sequences ◽  
And Function

The origin and activity of 45S rDNA located on micro B chromosomes of the daisy Brachycome dichromosomatica were analysed. The internal transcribed spacer 2 (ITS2) of the 45S rRNA gene was sequenced for micro B, large B, and A chromosomes of B. dichromosomatica cytodeme A2, and conserved differences were identified between sequences originating from A and both types of B chromosomes. Phylogenetic analysis did not identify a species containing an ITS2 sequence more similar to either of the B chromosome sequences than the B. dichromosomatica A chromosome sequences. Thus, an origin of the B chromosomes from A chromosomes at a time prior to the divergence of the 4 cytodemes of B. dichromosomatica is suggested. The frequent (70%) nucleolar non-association of micro B chromosomes suggests inactivity of micro B 45S rDNA.

Complete conversion of nitrate into dinitrogen gas in co-cultures of denitrifying bacteria

2005 ◽  
Vol 33 (1) ◽  
pp. 205-209 ◽  
Author(s):  
K.T. Van de Pas-Schoonen ◽  
S. Schalk-Otte ◽  
S. Haaijer ◽  
M. Schmid ◽  
H. Op den Camp ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Single Species ◽  
Alcaligenes Faecalis ◽  
Denitrifying Bacteria ◽  
Mixed Cultures ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Natural Ecosystems ◽  
Initial Work ◽  
Primer Sets

In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NOx reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.

scholarly journals Genetic markers associated with insecticide resistance and resting behaviour in Anopheles gambiae mosquitoes in selected sites in Kenya

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Sharon Mwagira-Maina ◽  
Steven Runo ◽  
Lucy Wachira ◽  
Stanley Kitur ◽  
Sarah Nyasende ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Anopheles Gambiae ◽  
Genetic Markers ◽  
Malaria Vector ◽  
Early Warning Systems ◽  
Chromosomal Inversion ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Resting Behaviour ◽  
Tana River

Abstract Background Molecular diagnostic tools have been incorporated in insecticide resistance monitoring programmes to identify underlying genetic basis of resistance and develop early warning systems of vector control failure. Identifying genetic markers of insecticide resistance is crucial in enhancing the ability to mitigate potential effects of resistance. The knockdown resistance (kdr) mutation associated with resistance to DDT and pyrethroids, the acetylcholinesterase-1 (ace-1R) mutation associated with resistance to organophosphates and carbamates and 2La chromosomal inversion associated with indoor resting behaviour, were investigated in the present study. Methods Anopheles mosquitoes sampled from different sites in Kenya and collected within the context of malaria vector surveillance were analysed. Mosquitoes were collected indoors using light traps, pyrethrum spray and hand catches between August 2016 and November 2017. Mosquitoes were identified using morphological keys and Anopheles gambiae sensu lato (s.l.) mosquitoes further identified into sibling species by the polymerase chain reaction method following DNA extraction by alcohol precipitation. Anopheles gambiae and Anopheles arabiensis were analysed for the presence of the kdr and ace-1R mutations, while 2La inversion was only screened for in An. gambiae where it is polymorphic. Chi-square statistics were used to determine correlation between the 2La inversion karyotype and kdr-east mutation. Results The kdr-east mutation occurred at frequencies ranging from 0.5 to 65.6% between sites. The kdr-west mutation was only found in Migori at a total frequency of 5.3% (n = 124). No kdr mutants were detected in Tana River. The ace-1R mutation was absent in all populations. The 2La chromosomal inversion screened in An. gambiae occurred at frequencies of 87% (n = 30), 80% (n = 10) and 52% (n = 50) in Baringo, Tana River and Migori, respectively. A significant association between the 2La chromosomal inversion and the kdr-east mutation was found. Conclusion The significant association between the 2La inversion karyotype and kdr-east mutation suggests that pyrethroid resistant An. gambiae continue to rest indoors regardless of the presence of treated bed nets and residual sprays, a persistence further substantiated by studies documenting continued mosquito abundance indoors. Behavioural resistance by which Anopheles vectors prefer not to rest indoors may, therefore, not be a factor of concern in this study’s malaria vector populations.

Placozoa: at least two

Biologia ◽  
2007 ◽  
Vol 62 (6) ◽  
Author(s):  
Matthias Wolf ◽  
Christian Selig ◽  
Tobias Müller ◽  
Nicole Philippi ◽  
Thomas Dandekar ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Internal Transcribed Spacer ◽  
Distinct Species ◽  
Secondary Structures ◽  
Its2 Sequence ◽  
Structure Alignment ◽  
Sequence Structure ◽  
Rna Sequence ◽  
Internal Transcribed Spacer 2 ◽  
Compensatory Base Changes

AbstractIt was shown that compensatory base changes (CBCs) in internal transcribed spacer 2 (ITS2) sequence-structure alignments can be used for distinguishing species. Using the ITS2 Database in combination with 4SALE — a tool for synchronous RNA sequence and secondary structure alignment and editing — in this study we present an in-depth CBC analysis for placozoan ITS2 sequences and their respective secondary structures. This analysis indicates at least two distinct species in Trichoplax (Placozoa) supporting a recently suggested hypothesis, that Placozoa is “no longer a phylum of one”.

Orthopodomyia pulcripalpis (Diptera: Culicidae), a genus and species new to the Iranian mosquito fauna, with a review of bionomical information*

Zootaxa ◽  
2017 ◽  
Vol 4299 (1) ◽  
pp. 141 ◽  
Author(s):  
SHAHYAD AZARI-HAMIDIAN ◽  
BEHZAD NOROUZI ◽  
AYOOB NOORALLAHI
Keyword(s):  
New Species ◽  
Aedes Albopictus ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its2 Sequence ◽  
Internal Transcribed Spacer 2 ◽  
As Species ◽  
Southwestern Iran ◽  
A New Species

The most recent checklist of Iranian mosquitoes (Diptera: Culicidae) includes 64 species representing seven genera (Azari-Hamidian, 2007; Azari-Hamidian & Harbach, 2009). Subsequently, Oshaghi et al. (2008) found that Anopheles superpictus Grassi is two species in Iran based on the Internal Transcribed Spacer 2 (ITS2) sequences of rDNA, which were later listed as species A and B by Harbach (2013), and Djadid et al. (2009) recognized a new species of the Anopheles hyrcanus group (An. hyrcanus spIR) from southwestern Iran, also based on ITS2 sequence data. More recently, Doosti et al. (2016) reported the occurrence of Aedes albopictus (Skuse) in southeastern Iran. 

Occurrence of true branches in Rhizoclonium (Cladophorales, Ulvophyceae) and the reinstatement of Rhizoclonium pachydermum Kjellman

Phytotaxa ◽  
2014 ◽  
Vol 166 (4) ◽  
pp. 273 ◽  
Author(s):  
ZHI-JUAN ZHAO ◽  
HUAN ZHU ◽  
ZHENG-YU HU ◽  
GUO-XIANG LIU
Keyword(s):  
Green Alga ◽  
Internal Transcribed Spacer ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
18S Rrna Gene ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Basal Region ◽  
Internal Transcribed Spacer 2

The phylogenetic position of the freshwater green alga Rhizoclonium pachydermum (Ulvophyceae: Cladophorales) was investigated using nuclear 18S rRNA gene and internal transcribed spacer 2 (ITS2) sequences. This alga has been referred to as Cladophora pachyderma. Based on its morphology, it was formerly classified in the section Affines in the genus Cladophora. However, this classification was not supported by the current phylogenetic analyses, where Rhizoclonium pachydermum formed a well-supported clade with other Rhizoclonium species. We consider that Rhizoclonium possesses real branches and the most important criteria that characterize the genus are: long unbranched filaments only with rhizoid branches, or only branched at the basal region of the thallus; and cylindrical cells with few or limited numbers of nuclei.

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