Characterization of the red knot (Calidris canutus) mitochondrial control region

Genome ◽  
2003 ◽  
Vol 46 (4) ◽  
pp. 565-572 ◽  
Author(s):  
Deborah M Buehler ◽  
Allan J Baker
Keyword(s):  
Control Region ◽  
Relative Rate ◽  
Mitochondrial Control Region ◽  
Single Individual ◽  
Future Studies ◽  
Calidris Canutus ◽  
Conserved Sequence ◽  
Significant Difference ◽  
D Loop ◽  
Control Regions

We sequenced the complete mitochondrial control regions of 11 red knots (Calidris canutus). The control region is 1168 bp in length and is flanked by tRNA glutamate (glu) and the gene ND6 at its 5' end and tRNA phenylalanine (phe) and the gene 12S on its 3' end. The sequence possesses conserved sequence blocks F, E, D, C, CSB-1, and the bird similarity box (BSB), as expected for a mitochondrial copy. Flanking tRNA regions show correct secondary structure, and a relative rate test indicated no significant difference between substitution rates in the sequence we obtained versus the known mitochondrial sequence of turnstones (Charadriiformes: Scolopacidae). These characteristics indicate that the sequence is mitochondrial in origin. To confirm this, we sequenced the control region of a single individual using both purified mitochondrial DNA and genomic DNA. The sequences were identical using both methods. The sequence and methods presented in this paper may now serve as a reference for future studies using knot and other avian control regions. Furthermore, the discovery of five variable sites in 11 knots towards the 3' end of the control region, and the variability of this region in contrast to the more conserved central domain in the alignment between knots and other Charadriiformes, highlights the importance of this area as a source of variation for future studies in knots and other birds.Key words: D-loop, Calidris canutus, Charadriiformes, Aves, evolution.

A repeat complex in the mitochondrial control region of Adélie penguins from Antarctica

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 613-618 ◽  
Author(s):  
Peter A Ritchie ◽  
David M Lambert
Keyword(s):  
Control Region ◽  
Mitochondrial Control Region ◽  
Adélie Penguin ◽  
Pygoscelis Adeliae ◽  
Adelie Penguin ◽  
Conserved Sequence ◽  
Repeat Sequences ◽  
Associated Sequences ◽  
Microsatellite Evolution ◽  
D Loop

We have determined the nucleotide sequence of the entire mitochondrial control region (CR) of the Adélie penguin (Pygoscelis adeliae) from Antarctica. Like in most other birds, this CR region is flanked by the gene nad6 and transfer (t)RNA trnE(uuc) at the 5' end and the gene rns and trnF(gaa) at the 3' end. Sequence analysis shows that the Adélie penguin CR contains many elements in common with other CRs including the termination associated sequences (TAS), conserved F, E, D, and C boxes, the conserved sequence block (CSB)-1, as well as the putative light and heavy strand promoters sites (LSP-HSP). We report an extraordinarily long avian control region (1758 bp) which can be attributed to the presence, at the 3' peripheral domain, of five 81-bp repeat sequences, each containing a putative LSP-HSP, followed by 30 tetranucleotide microsatellite repeat sequences consisting of (dC-dA-dA-dA)30. The microsatellite and the 81-bp repeat reside in an area known to be transcribed in other species.Key words: Aves, microsatellite, evolution, D-loop, TAS, WANCY.

scholarly journals A molecular characteristic of the Anatidae mitochondrial control region – a review

2018 ◽  
Vol 18 (1) ◽  
pp. 3-15 ◽  
Author(s):  
Joanna Warzecha ◽  
Agnieszka Fornal ◽  
Maria Oczkowicz ◽  
Monika Bugno-Poniewierska
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Control Region ◽  
Close Relationships ◽  
Genetic Research ◽  
Mitochondrial Control Region ◽  
Coding Region ◽  
Conserved Domain ◽  
Control Region Sequences ◽  
D Loop

Abstract Mitochondrial DNA (mtDNA) is a molecular tool that is very effective in genetic research, including phylogenetic analysis. The non-coding region is the most variable fragment of mtDNA, showing variability in length and nucleobase composition and containing three domains: two hypervariable peripheral regions and the conserved domain (D-loop) in the middle. The Anseriformes are amongst the best studied avian groups, including approximately 150 species and containing geese, swans, ducks (Anatidae), the Magpie goose (Anseranatidae) and screamers (Anhimidae). The most numerous family is the Anatidae, appearing in close relationships within the phylogenetic branches of the species. There are differences between the non-coding region of the Anatidae in comparison to other avian control regions. In the article presented below the control region sequences and the phylogeny of the Anatidae were reviewed.

A very compact mt-DNA control region in the widely distributed goby Pomatoschistus minutus (Teleostei: Gobiidae)

2002 ◽  
Vol 82 (6) ◽  
pp. 1001-1003 ◽  
Author(s):  
S. STEFANNI ◽  
I.-S. CHEN ◽  
P.J. MILLER
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Sequence Divergence ◽  
Mt Dna ◽  
Conserved Sequence ◽  
Sequence Block ◽  
Pomatoschistus Minutus ◽  
Region Length ◽  
D Loop

The control region of the mitochondrial genome was amplified and sequenced for six individuals of the gobioid fish Pomatoschistus minutus, from several European localities, and one specimen of the related Deltentosteus quadrimaculatus. The length of this region for the former species was found to be 773 bp, 7·1% shorter than that previously described as the most compact D-loop known among teleosts. Sequences from other fish have been compared and the largest gap falls in the section between the conserved sequence block and the pyrimidine tract. Alignment of P. minutus sequences was done with D. quadrimaculatus, whose control region length was 853 bp, and this gap was found to be of 61 bp. For the P. minutus sample, the intraspecific sequence divergence is 0·07%.

Polyzosteria cockroaches in Tasmania (Blattodea: Blattidae: Polyzosteriinae) represent a new, endemic species, with allopatric alpine and coastal sub-populations

Zootaxa ◽  
2021 ◽  
Vol 4926 (3) ◽  
pp. 384-400
Author(s):  
SHASTA C. HENRY ◽  
STEPHEN L. CAMERON ◽  
ADAM SMOLENSKI ◽  
PETER MCQUILLAN
Keyword(s):  
Molecular Analysis ◽  
Control Region ◽  
Endemic Species ◽  
Single Species ◽  
Mitochondrial Control Region ◽  
Species Identity ◽  
Allopatric Populations ◽  
Unusual Distribution ◽  
Alpine Population ◽  
D Loop

We describe the endemic Tasmanian cockroach, Polyzosteria yingina sp. nov. (Henry), 78 years after it was first documented. Evidence from morphology, biogeography and CO1 barcodes is used to distinguish this species from related mainland Australian taxa it has previously been confused with. Polyzosteria yingina sp. nov. has two strongly allopatric populations: a compact alpine population above 1000m and a dispersed east coastal one at sealevel. However, mitochondrial Control Region D-loop molecular analysis suggests a single species identity for these disparate populations. Detailed internal and external morphological descriptions and photographs of living and preserved type material are presented. We also speculate on some hypotheses which could account for the unusual distribution of this charismatic insect. 

Tandemly repeated sequences in mtDNA control region of whitefish, Coregonus lavaretus

Genome ◽  
2000 ◽  
Vol 43 (3) ◽  
pp. 584-587 ◽  
Author(s):  
Pawel Brzuzan
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Pcr Amplification ◽  
Repeated Sequences ◽  
Coregonus Lavaretus ◽  
Length Variation ◽  
Conserved Sequence ◽  
Repeat Units ◽  
Pcr Products ◽  
D Loop

Length variation of the mitochondrial DNA control region was observed with PCR amplification of a sample of 138 whitefish (Coregonus lavaretus). Nucleotide sequences of representative PCR products showed that the variation was due to the presence of an approximately 100-bp motif tandemly repeated two, three, or five times in the region between the conserved sequence block-3 (CSB-3) and the gene for phenylalanine tRNA. This is the first report on the tandem array composed of long repeat units in mitochondrial DNA of salmonids.Key words: Coregonus lavaretus, D-loop mitochondrial DNA, tandemly repeated sequences.

Molecular population phylogeny of the hazel grouseBonasa bonasiain East Asia inferred from mitochondrial control-region sequences

2002 ◽  
Vol 8 (1) ◽  
pp. 251-259 ◽  
Author(s):  
Yoshiyuki Baba ◽  
Yuzo Fujimaki ◽  
Siegfried Klaus ◽  
Olga Butorina ◽  
Serguei Drovetskii ◽  
...  
Keyword(s):  
East Asia ◽  
Control Region ◽  
Mitochondrial Control Region ◽  
Control Region Sequences

scholarly journals 551. Convalescent plasma early in disease course improves survival in COVID-19

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S341-S342
Author(s):  
Varidhi Nauriyal ◽  
Anita Shallal ◽  
Amit T Vahia ◽  
Linoj Samuel ◽  
Robert Tibbetts ◽  
...  
Keyword(s):  
Scale Score ◽  
Medical Records ◽  
Clinical Status ◽  
Ordinal Scale ◽  
Optimal Timing ◽  
Care Hospital ◽  
Future Studies ◽  
Patient Gender ◽  
Significant Difference ◽  
Pcr Test

Abstract Background Convalescent plasma (CP) has been described as a potential therapy for coronavirus disease 2019 (COVID-19). Given paucity of data, we sought to describe characteristics of CP recipients in survivors and non-survivors. Methods We conducted retrospective review of electronic medical records which included any patient with a positive SARS-CoV-2 PCR test who received CP at an 890-bed quaternary care hospital in Southeast Michigan between March-May 2020. Data collected included: demographics, co-morbidities, mSOFA score on admission, laboratory values, and treatment. Outcomes assessed included inflammatory markers and clinical status based on an 8-point ordinal scalea. These values were recorded on admission, the date of CP (day 1), day 3, 7, and day 30 post-CP. Patient outcomes were stratified by ordinal scale score and compared using Mann-Whitney U tests to examine differences in clinical characteristics: scale of 1–4 (“meaningful survivor”), 5–7 (“survivor”), and 8 (“non-survivor”). Results Results of our study are summarized in Table 1 and 2. Non-survivors were older than survivors (62 vs 71 years; p=0.026). There was no statistically significant difference between patient gender, race, number of days from positive PCR test to CP, treatments, and co-morbidities. There was a trend toward higher mSOFA score on admission in non-survivors (p=0.056). A lower ordinal scale score on the date of receiving CP was significantly associated with meaningful survivorship (6 vs 7, p=0.005). Comparisons of Characteristics Based on Ordinal Scale at Day 30 Comparisons of Outcomes Based on Ordinal Scale at Day 30 Conclusion Patients who have a lower ordinal scale score on the date of CP administration are most likely to have meaningful survivorship at day 30. Future studies should evaluate optimal timing and outcomes for CP therapy in COVID-19. Disclosures All Authors: No reported disclosures

scholarly journals “Les copains *dit au revoir”: On Subject–Verb Agreement in L2 French and Cross-Linguistic Influence

Languages ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 7
Author(s):  
Malin Ågren ◽  
Marie-Eve Michot ◽  
Cyrille Granget ◽  
Sonia Gerolimich ◽  
Pascale Hadermann ◽  
...  
Keyword(s):  
Second Language Acquisition ◽  
Oral Narrative ◽  
Complex Interplay ◽  
Verb Morphology ◽  
Future Studies ◽  
Proficiency Levels ◽  
Verb Agreement ◽  
Significant Difference ◽  
L2 Development

This study focuses on the production of subject–verb (SV) agreement in number in L2 French and investigates the role of cross-linguistic influence (CLI) in this particular morphosyntactic domain. CLI is a well-known phenomenon in Second Language Acquisition (SLA) research but it has rarely been investigated systematically in relation to SV agreement in French. The participants of the study are 114 learners with Italian, German, Dutch and Swedish as L1. The source languages are all inflectional languages but they vary in terms of morphological richness in the verb paradigm, ranging from very poor (Swedish) to very rich (Italian). The participants performed an oral narrative task contrasting singular and plural contexts of SV agreement. Results indicate a significant difference between L1 groups in terms of correct SV agreement but they also show that the overall presence of rich verb morphology in the L1 does not, on its own, result in a more correct SV agreement. It is when comparing learners at two different proficiency levels that we observe differences in the rate of L2 development, which may be explained as an effect of CLI. Overall, results indicate a complex interplay of different factors, where the role of CLI must be further investigated in future studies in relation to L2 French.

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