scholarly journals The mitochondrial genome of the pathogenic yeast Candida subhashii: GC-rich linear DNA with a protein covalently attached to the 5′ termini

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2153-2163 ◽  
Author(s):  
Dominika Fricova ◽  
Matus Valach ◽  
Zoltan Farkas ◽  
Ilona Pfeiffer ◽  
Judit Kucsera ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Large Scale ◽  
Dna Polymerases ◽  
Specific Primers ◽  
Pathogenic Yeast ◽  
Unknown Protein ◽  
The Family ◽  
Linear Dsdna ◽  
Linear Molecules ◽  
Terminal Proteins

As a part of our initiative aimed at a large-scale comparative analysis of fungal mitochondrial genomes, we determined the complete DNA sequence of the mitochondrial genome of the yeast Candida subhashii and found that it exhibits a number of peculiar features. First, the mitochondrial genome is represented by linear dsDNA molecules of uniform length (29 795 bp), with an unusually high content of guanine and cytosine residues (52.7 %). Second, the coding sequences lack introns; thus, the genome has a relatively compact organization. Third, the termini of the linear molecules consist of long inverted repeats and seem to contain a protein covalently bound to terminal nucleotides at the 5′ ends. This architecture resembles the telomeres in a number of linear viral and plasmid DNA genomes classified as invertrons, in which the terminal proteins serve as specific primers for the initiation of DNA synthesis. Finally, although the mitochondrial genome of C. subhashii contains essentially the same set of genes as other closely related pathogenic Candida species, we identified additional ORFs encoding two homologues of the family B protein-priming DNA polymerases and an unknown protein. The terminal structures and the genes for DNA polymerases are reminiscent of linear mitochondrial plasmids, indicating that this genome architecture might have emerged from fortuitous recombination between an ancestral, presumably circular, mitochondrial genome and an invertron-like element.

scholarly journals Duplication of a Truncated Paralog of the Family B DNA Polymerase Gene Aa-polB in the Agrocybe aegerita Mitochondrial Genome

2001 ◽  
Vol 67 (4) ◽  
pp. 1739-1743 ◽  
Author(s):  
Gerard Barroso ◽  
Frederic Bois ◽  
Jacques Labarère
Keyword(s):  
Mitochondrial Genome ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Polymerase Gene ◽  
Mitochondrial Trna ◽  
Amino Acid Similarity ◽  
Agrocybe Aegerita ◽  
Naturally Occurring ◽  
The Family ◽  
Dna Polymerase Gene

ABSTRACT The Agrocybe aegerita mitochondrial genome contains a truncated family B DNA polymerase gene (Aa-polB P1) whose nucleotide sequence is 86% identical to the previously described and potentially functional Aa-polB gene. A tRNAMetgene occurs at the 3′ end of the Aa-polB P1 gene. TheAa-polB P1 gene could result from reverse transcription of an Aa-polB mRNA primed by a tRNAMet followed by the integration of the cDNA after recombination at the mitochondrial tRNA locus. Two naturally occurring alleles of Aa-polB P1carry one or two copies of the disrupted sequence. In strains with two copies of Aa-polB P1, these copies are inverted relative to one another and separated by a short sequence carrying the tRNAMet gene. Both A. aegerita mitochondrial family B DNA polymerases were found to be related to other family B DNA polymerases (36 to 53% amino acid similarity), including the three enzymes of the archaebacterium Sulfolobus solfataricus. If mitochondria originated from a fusion between aClostridium-like eubacterium and aSulfolobus-like archaebacterium, then the A. aegerita family B DNA polymerase genes could be remnants of the archaebacterial genes.

scholarly journals Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7669 ◽  
Author(s):  
Sébastien Leveque ◽  
Lutfi Afiq-Rosli ◽  
Yin Cheong Aden Ip ◽  
Sudhanshi S. Jain ◽  
Danwei Huang
Keyword(s):  
Community Structure ◽  
Host Species ◽  
Large Scale ◽  
Coral Host ◽  
Specific Primers ◽  
Closely Related Species ◽  
Phylogenetic Constraint ◽  
Stony Corals ◽  
The Family ◽  
Dna Metabarcoding

Over half of all extant stony corals (Cnidaria: Anthozoa: Scleractinia) harbour endosymbiotic dinoflagellates of the family Symbiodiniaceae, forming the foundational species of modern shallow reefs. However, whether these associations are conserved on the coral phylogeny remains unknown. Here we aim to characterise Symbiodiniaceae communities in eight closely-related species in the genera Merulina, Goniastrea and Scapophyllia, and determine if the variation in endosymbiont community structure can be explained by the phylogenetic relatedness among hosts. We perform DNA metabarcoding of the nuclear internal transcribed spacer 2 using Symbiodiniaceae-specific primers on 30 coral colonies to recover three major endosymbiont clades represented by 23 distinct types. In agreement with previous studies on Southeast Asian corals, we find an abundance of Cladocopium and Durusdinium, but also detect Symbiodinium types in three of the eight coral host species. Interestingly, differences in endosymbiont community structure are dominated by host variation at the intraspecific level, rather than interspecific, intergeneric or among-clade levels, indicating a lack of phylogenetic constraint in the coral-endosymbiont association among host species. Furthermore, the limited geographic sampling of four localities spanning the Western and Central Indo-Pacific preliminarily hints at large-scale spatial structuring of Symbiodiniaceae communities. More extensive collections of corals from various regions and environments will help us better understand the specificity of the coral-endosymbiont relationship.

scholarly journals Species-Specific Primers for Eutypella parasitica, the Causal Agent of Eutypella Canker of Maple

Plant Disease ◽  
2007 ◽  
Vol 91 (12) ◽  
pp. 1579-1584 ◽  
Author(s):  
Barbara Piškur ◽  
Nikica Ogris ◽  
Dušan Jurc
Keyword(s):  
Large Scale ◽  
Fragment Size ◽  
Intraspecific Variability ◽  
Its Region ◽  
Specific Primers ◽  
Eutypa Lata ◽  
Wide Range ◽  
The Family ◽  
Species Specific ◽  
First Time

Eutypella parasitica was recently reported in Europe for the first time, and this study reports the molecular evaluation of the internal transcribed spacer (ITS)1/5.8S/ITS2 regions of 68 isolates of the fungus obtained in pure culture with polymerase chain reaction restriction fragment length polymorphism (RFLP). The RFLP patterns of all isolates proved identical and the restriction profiles served to differentiate E. parasitica from Eutypa lata, another pathogenic member of the family Diatrypaceae. Low intraspecific variability was detected in the sequenced ITS1/5.8S/ITS2 regions of eight Eutypella parasitica isolates originating from different hosts and geographical locations. Based on this ITS region, EpR/F primers specific to E. parasitica were constructed and tested with a wide range of fungal isolates. The EpR/F primer pair successfully amplified the expected fragment size of 341 bp from isolates of E. parasitica and also directly from infected maple wood shavings. The RFLP patterns and species-specific primers represent a step toward routine, large-scale, and rapid molecular diagnostics and identification of E. parasitica.

A Family With Autosomal-Dominant Progressive Sensorineural Hearing Loss

1996 ◽  
Vol 5 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Chris Halpin ◽  
Barbara Herrmann ◽  
Margaret Whearty
Keyword(s):  
Speech Production ◽  
Hearing Aids ◽  
Role Models ◽  
Speech Intelligibility ◽  
Large Scale ◽  
Speech Language Pathology ◽  
The Family ◽  
Patient Will ◽  
Language Pathology

The family described in this article provides an unusual opportunity to relate findings from genetic, histological, electrophysiological, psychophysical, and rehabilitative investigation. Although the total number evaluated is large (49), the known, living affected population is smaller (14), and these are spread from age 20 to age 59. As a result, the findings described above are those of a large-scale case study. Clearly, more data will be available through longitudinal study of the individuals documented in the course of this investigation but, given the slow nature of the progression in this disease, such studies will be undertaken after an interval of several years. The general picture presented to the audiologist who must rehabilitate these cases is that of a progressive cochlear degeneration that affects only thresholds at first, and then rapidly diminishes speech intelligibility. The expected result is that, after normal language development, the patient may accept hearing aids well, encouraged by the support of the family. Performance and satisfaction with the hearing aids is good, until the onset of the speech intelligibility loss, at which time the patient will encounter serious difficulties and may reject hearing aids as unhelpful. As the histological and electrophysiological results indicate, however, the eighth nerve remains viable, especially in the younger affected members, and success with cochlear implantation may be expected. Audiologic counseling efforts are aided by the presence of role models and support from the other affected members of the family. Speech-language pathology services were not considered important by the members of this family since their speech production developed normally and has remained very good. Self-correction of speech was supported by hearing aids and cochlear implants (Case 5’s speech production was documented in Perkell, Lane, Svirsky, & Webster, 1992). These patients received genetic counseling and, due to the high penetrance of the disease, exhibited serious concerns regarding future generations and the hope of a cure.

The Use of Medical Record Linkage for Population and Genetic Studies

1969 ◽  
Vol 08 (01) ◽  
pp. 07-11 ◽  
Author(s):  
H. B. Newcombe
Keyword(s):  
Record Linkage ◽  
Large Scale ◽  
Medical Record Linkage ◽  
Canadian Province ◽  
Genetic Studies ◽  
Parental Characteristics ◽  
Family Histories ◽  
The Family ◽  
Large Populations ◽  
Machine Readable

Methods are described for deriving personal and family histories of birth, marriage, procreation, ill health and death, for large populations, from existing civil registrations of vital events and the routine records of ill health. Computers have been used to group together and »link« the separately derived records pertaining to successive events in the lives of the same individuals and families, rapidly and on a large scale. Most of the records employed are already available as machine readable punchcards and magnetic tapes, for statistical and administrative purposes, and only minor modifications have been made to the manner in which these are produced.As applied to the population of the Canadian province of British Columbia (currently about 2 million people) these methods have already yielded substantial information on the risks of disease: a) in the population, b) in relation to various parental characteristics, and c) as correlated with previous occurrences in the family histories.

AFLP-derived, Codominant Markers for Locus-specific Applications

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 514e-514
Author(s):  
James M. Bradeen ◽  
Philipp W. Simon
Keyword(s):  
Linkage Mapping ◽  
Large Scale ◽  
Pcr Primers ◽  
Inverse Pcr ◽  
Sequence Information ◽  
Pcr Assay ◽  
Specific Primers ◽  
Simultaneous Evaluation ◽  
Feral Populations ◽  
Diversity Assessment

The amplified fragment length polymorphism (AFLP) is a powerful marker, allowing rapid and simultaneous evaluation of multiple potentially polymorphic sites. Although well-adapted to linkage mapping and diversity assessment, AFLPs are primarily dominant in nature. Dominance, relatively high cost, and technological difficulty limit use of AFLPs for marker-aided selection and other locus-specific applications. In carrot the Y2 locus conditions carotene accumulation in the root xylem. We identified AFLP fragments linked to the dominant Y2 allele and pursued conversion of those fragments to codominant, PCR-based forms useful for locus-specific applications. The short length of AFLPs (≈60 to 500 bp) precludes development of longer, more specific primers as in SCAR development. Instead, using sequence information from cloned AFLP fragments for primer design, regions outside of the original fragment were amplified by inverse PCR or ligation-mediated PCR, cloned, and sequenced. Differences in sequences associated with Y2 vs. y2 allowed development of simple PCR assays differentiating those alleles. PCR primers flanking an insertion associated with the recessive allele amplified differently sized products for the two Y2 alleles in one assay. This assay is rapid, technologically simple (requiring no radioactivity and little advanced training or equipment), reliable, inexpensive, and codominant. Our PCR assay has a variety of large scale, locus-specific applications including genotyping diverse carrot cultivars and wild and feral populations. Efforts are underway to improve upon conversion technology and to more extensively test the techniques we have developed.

scholarly journals Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alisa Alekseenko ◽  
Donal Barrett ◽  
Yerma Pareja-Sanchez ◽  
Rebecca J. Howard ◽  
Emilia Strandback ◽  
...  
Keyword(s):  
Large Scale ◽  
Direct Detection ◽  
Dna Polymerases ◽  
Scale Up ◽  
Lamp Assay ◽  
Cost Effective ◽  
Reaction Conditions ◽  
Clinical Patient ◽  
Reverse Transcriptases ◽  
Large Scale Testing

AbstractRT-LAMP detection of SARS-CoV-2 has been shown to be a valuable approach to scale up COVID-19 diagnostics and thus contribute to limiting the spread of the disease. Here we present the optimization of highly cost-effective in-house produced enzymes, and we benchmark their performance against commercial alternatives. We explore the compatibility between multiple DNA polymerases with high strand-displacement activity and thermostable reverse transcriptases required for RT-LAMP. We optimize reaction conditions and demonstrate their applicability using both synthetic RNA and clinical patient samples. Finally, we validate the optimized RT-LAMP assay for the detection of SARS-CoV-2 in unextracted heat-inactivated nasopharyngeal samples from 184 patients. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings where the need for large scale testing cannot be met by commercial alternatives.

Abstract 17081: End Stage Mitochondrial Cardiomyopathy And Heart Transplantation Due To Pathogenic Biallelic C1QBP Variants

Circulation ◽  
2021 ◽  
Vol 144 (Suppl_2) ◽  
Author(s):  
Nicholas S Wilcox ◽  
Stuart Prenner ◽  
Marisa Cevasco ◽  
Courtney Condit ◽  
Amy Goldstein ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Heart Transplantation ◽  
Genome Sequencing ◽  
Large Scale ◽  
De Novo ◽  
Late Onset ◽  
Genetic Disorder ◽  
Disease Onset ◽  
Serum Lactate ◽  
Metabolic Decompensation

Case Presentation: A 29-year-old male with LVH diagnosed in childhood was admitted with acute HF. TTE showed LVEF 5-10% and LV thrombi for which he was anticoagulated. He received inappropriate ICD shocks due to T wave oversensing, leading to cardiogenic shock requiring VA-ECMO support. Serum lactate peaked at 17 mmol/L due to cardiac and metabolic decompensation. He underwent heart transplantation (HT) on hospital day (HD) 8 and tolerated standard immunosuppression. First endomyocardial biopsy showed acute cellular rejection requiring pulse steroids. He was discharged on HD 33. Trio whole exome and mitochondrial genome sequencing revealed biallelic variants in complement component 1Q subcomponent-binding protein ( C1QBP ), due to a maternally inherited likely pathogenic variant c.612C>G (p.F204L in exon 5) and an apparently de novo deletion of 17p13.2, spanning exons 4-6 of C1QBP and exon 6 of the RPAIN gene. Mitochondrial genome sequencing of the explanted heart revealed multiple large-scale mitochondrial DNA deletions at 33% heteroplasmy. Discussion: C1QBP variants are associated with mitochondrial and multi-organ dysfunction. Only 12 patients exhibiting biallelic C1QBP variants are reported. Four died in the peripartum period due to fetal hydrops or HF; 5 exhibited early-onset cardiomyopathy (CM); 3 others had late-onset ophthalmoplegia without CM. The p.F204L variant has been reported in 1 patient with compound C1QBP p.F204L/p.C186S heterozygosity who died from hydrops fetalis and a second with p.F204L homozygosity with late-onset ophthalmoplegia and skeletal myopathy without CM. Differences in the size, heteroplasmy, and tissue distribution of mitochondrial genome secondary deletions may explain variability in disease onset and progression. We present the first patient with biallelic pathogenic C1QBP gene variants with mitochondrial CM to undergo HT and highlight the diagnosis and management of an exceptionally uncommon genetic disorder.

Complete Mitochondrial Genome Sequence Analysis and Phylogenetic Location Determination of Hydropsyche Fryeri (Insecta: Trichoptera)

2021 ◽  
Author(s):  
Yimin Li ◽  
Honglin Qin ◽  
Xifa Zhong ◽  
Jingcai Huang ◽  
Yujun Wang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequence ◽  
Complete Mitochondrial Genome ◽  
Phylogenetic Tree Analysis ◽  
Protein Coding ◽  
Mitochondrial Genome Sequence ◽  
Complete Mitochondrial Genome Sequence ◽  
Location Determination ◽  
The Family

Abstract Hydropsyche fryeri belongs to the Trichopteridae family and builds nests in clean and unpolluted streams using stones. It also can be used as an indicator of water quality. Here, we describe the complete mitochondrial genome sequence of Hydropsyche fryeri. The mitochondrial genome is 15,676 bp long and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and an AT-rich control region. Phylogenetic tree analysis shows that Hydropsyche fryeri is more closely related to the family Hydroptera than other Trichoptera.

scholarly journals An assessment of the population status of the threatened medicinal plant Illicium griffithii Hook.f. & Thomson in West Kameng District of Arunachal Pradesh, India

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Tashi Dorjee Bapu ◽  
Gibji Nimasow
Keyword(s):  
Medicinal Plant ◽  
Large Scale ◽  
Arunachal Pradesh ◽  
Mature Trees ◽  
Regeneration Rate ◽  
Dead Trees ◽  
Threatened Medicinal Plant ◽  
The Family ◽  
Proper Training ◽  
Large Scale Cultivation

Illicium griffithii Hook.f. & Thomson, a medicinal plant of the family Schisandraceae, is an Endangered species listed by the IUCN.  A decline in population of this plant due to climate change as well as increasing human influences on the natural resources has been a matter of great concern among the researchers.  In order to estimate the existing population of this plant, a field-based study employing linear transect method was conducted in four phases, May–June 2017, May–June 2018, April–May 2019, October–November 2019 covering an area of 700km² (approx.) in West Kameng District of Arunachal Pradesh that lies within the Himalayan biodiversity hotspot.  The study recorded 3,044 live individuals of I. griffithii including 1,372 seedlings, 1,358 saplings, and only 314 mature trees.  Additionally, 126 dead trees were also recorded.  The study confirmed that the plant has a good regeneration rate but with a poor survival rate of saplings.  Besides, large-scale collection of its fruits for trade and anthropogenic disturbances in the study area appears to be the major threat to its existing population.  Therefore, proper training of the local people on large-scale cultivation of this plant together with awareness towards judicious harvesting of fruits from the wild may be the significant approach to conservation. 

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