Mitochondrial Sequence Variation, Haplotype Diversity, and Relationships Among Dromedary Camel-Types

Dromedary camels are outstanding livestock that developed efficient abilities to tolerate desert conditions. Many dromedary camel-types (i.e., named populations) exist but lack defined specific breed standards, registries, and breeders’ governing organizations. The breed status of dromedary camel-types can partly be assessed by exploring mitochondrial DNA (mtDNA) variation. Accordingly, this study aimed to examine the breed status and the inter-population relationships of dromedary camel-types by analyzing sequence variation in the mtDNA control region and in three coding genes [cytochrome b, threonine, and proline tRNA, and part of the displacement loop (D-loop)] (867 bp region). Tail hair samples (n = 119) that represent six camel-types from Kuwait were collected, extracted, sequenced, and compared to other publicly available sequences (n = 853). Within the sequenced mitochondrial region, 48 polymorphic sites were identified that contributed to 82 unique haplotypes across 37 camel-types. Haplotype names and identities were updated to avoid previous discrepancies. When all sequences were combined (n = 972), a nucleotide diversity of 0.0026 and a haplotype diversity of 0.725 was observed across the dromedary-types. Two major haplogroups (A and B) were identified and the B1 haplotype was predominant and found in almost all dromedary-types whereas the A haplotypes were more abundant in African regions. Non-metric multidimensional scaling revealed an increased similarity among Arabian Peninsula “Mezayen” camel-types, despite their defining coat colors. The relationships among dromedary camel-types can partly be explained by mtDNA. Future work aimed at a deeper understanding of camel-type breed status should focus on a high number of nuclear markers.

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Mitochondrial DNA-based diversity study of Hungarian brown hares (Lepus europaeus Pallas 1778)

Acta Agraria Debreceniensis ◽

10.34101/actaagrar/69/1783 ◽

2016 ◽

pp. 23-29

Author(s):

Noémi Soós ◽

Szilvia Kusza

Keyword(s):

Mitochondrial Dna ◽

Large Scale ◽

Haplotype Diversity ◽

Lepus Europaeus ◽

Brown Hare ◽

High Genetic Diversity ◽

Ongoing Research ◽

European Continent ◽

Hair Samples ◽

D Loop

The brown hare being an important game species which is widespread across the European continent has been in focus of many population genetic studies. However only a few comprising researches can be found on the diversity of Central-European populations. The aim of our large scale long term ongoing study is to fill this gap of information on the species by describing the genetic history and structure of the brown hare populations of the area using both mitochondrial DNA markers and genomic skin and hair colour regulating genes. This article gives forth a part of our results concerning the mitochondrial DNA diversity of Hungarian brown hares based on amplification of a 512 bp long D-loop sequence. N=39 tissue or hair samples have been collected from 15 sampling sites on the Hungarian Great Plain. We have described a high level of haplotype diversity (Hd=0.879±0.044) based on a 410 bp alignment of our sequences. We have found 17 haplotypes within our sample set with the nucleotid diversity of π=0.01167±0.0022. Our ongoing research shows high genetic diversity for the brown hare in the studied region and a second alignment with 156 sequences downloaded from GenBank indicates a geographic pattern of haplotypes among the studied populations though these results need confirmation by our further analyses.

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Genetic variability of Akhal-Teke horses bred in Italy

PeerJ ◽

10.7717/peerj.4889 ◽

2018 ◽

Vol 6 ◽

pp. e4889

Author(s):

Maria C. Cozzi ◽

Maria G. Strillacci ◽

Paolo Valiati ◽

Elisa Rogliano ◽

Alessandro Bagnato ◽

...

Keyword(s):

Genetic Variability ◽

Haplotype Diversity ◽

Principal Component ◽

Italian Population ◽

Horse Population ◽

Loop Region ◽

Marker Loci ◽

D Loop ◽

Inbreeding Level ◽

Almost All

Background The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. Methods Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences. Results Nucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.

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High Intraspecific Genetic Diversity ofNocardia brasiliensis, a Pathogen Responsible for Cutaneous Nocardiosis Found in France: Phylogenetic Relationships by Usingsodandhsp65Genes

BioMed Research International ◽

10.1155/2018/7314054 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10

Author(s):

D. Kosova-Maali ◽

E. Bergeron ◽

Y. Maali ◽

T. Durand ◽

J. Gonzalez ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Genetic Characterization ◽

Haplotype Diversity ◽

Species Level ◽

Genotype 1 ◽

Tropical Regions ◽

High Bootstrap ◽

Almost All ◽

A New Species ◽

Immunocompetent Patients

This study aims at genetic characterization and phylogenetic relationships ofNocardia brasiliensisfocusing by using housekeepingrrs,hsp65,andsodAgenes.N. brasiliensisis the species responsible for 80% of cases of actinomycetoma, one form of cutaneous nocardiosis which occurs mainly in tropical regions reaching immunocompetent patients in which the disease can lead to amputation. We analyze 36 indigenous cases ofN. brasiliensisthat happened in France. Phylogenetic analysis targetingrrsgene showed no robustness at phylogenetic nodes level. However, the use of a concatenation ofhsp65andsodAgenes showed that the tested strains surprisingly ranked in 3 well-defined genotypes. Genotypes 2 and 3 were phylogenetically closer to each other and both diverged from genotype 1 sustained by a high bootstrap of 81%. This last genotype hosts all the cases of pulmonary forms (3), the sole cerebral form, and almost all the cases of immunocompromised patients (3 out of 4). Moreover, excepting one of them, all the strains belonging to this group present a susceptibility to imipenem which is not the case in the other genotypes that rarely count among them strains being susceptible to this drug. The haplotype diversity (Hd) ofhsp65(0.927) andsodA(0.885) genes was higher than that ofrrs(0.824). For this gene, we obtained 16 polymorphic sites whereas, forhsp65andsodAgenes, up to 27 and 29 were identified, respectively. This study reveals that these two genes have an important genetic discriminatory power for the evaluation of the intraspecies genetic variability ofN. brasiliensisand they may be useful for identification purposes at species level. This study also reveals the possible existence of a new species harbored by genotype 1.

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Sequence variation and structural conservation in the D-loop region and flanking genes of mitochondrial DNA from Japanese pond frogs.

Genes & Genetic Systems ◽

10.1266/ggs.75.79 ◽

2000 ◽

Vol 75 (2) ◽

pp. 79-92 ◽

Cited By ~ 18

Author(s):

Masayuki Sumida ◽

Hideki Kaneda ◽

Yoji Kato ◽

Yasushi Kanamori ◽

Hiromichi Yonekawa ◽

...

Keyword(s):

Mitochondrial Dna ◽

Sequence Variation ◽

Loop Region ◽

D Loop ◽

Structural Conservation

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Characterising ICU–ward handoffs at three academic medical centres: process and perceptions

BMJ Quality & Safety ◽

10.1136/bmjqs-2018-008328 ◽

2019 ◽

Vol 28 (8) ◽

pp. 627-634 ◽

Cited By ~ 5

Author(s):

Lekshmi Santhosh ◽

Patrick G Lyons ◽

Juan C Rojas ◽

Thomas M Ciesielski ◽

Shire Beach ◽

...

Keyword(s):

Adverse Event ◽

Best Practices ◽

Teaching Hospitals ◽

Process Maps ◽

Diagnostic Uncertainty ◽

Academic Medical ◽

Multimodal Methods ◽

Almost All ◽

Rehabilitation Needs ◽

Future Work

BackgroundThere is limited literature about physician handoffs between the intensive care unit (ICU) and the ward, and best practices have not been described. These patients are uniquely vulnerable given their medical complexity, diagnostic uncertainty and reduced monitoring intensity. We aimed to characterise the structure, perceptions and processes of ICU–ward handoffs across three teaching hospitals using multimodal methods: by identifying the handoff components involved in communication failures and describing common processes of patient transfer.MethodsWe conducted a study at three academic medical centres using two methods to characterise the structure, perceptions and processes of ICU–ward transfers: (1) an anonymous resident survey characterising handoff communication during ICU–ward transfer, and (2) comparison of process maps to identify similarities and differences between ICU–ward transfer processes across the three hospitals.ResultsOf the 295 internal medicine residents approached, 175 (59%) completed the survey. 87% of the respondents recalled at least one adverse event related to communication failure during ICU–ward transfer. 95% agreed that a well-structured handoff template would improve ICU–ward transfer. Rehabilitation needs, intravenous access/hardware and risk assessments for readmission to the ICU were the most frequently omitted or incorrectly communicated components of handoff notes. More than 60% of the respondents reported that notes omitted or miscommunicated pending results, active subspecialty consultants, nutrition and intravenous fluids, antibiotics, and healthcare decision-maker information at least twice per month. Despite variable process across the three sites, all process maps demonstrated flaws and potential for harm in critical steps of the ICU–ward transition.ConclusionIn this multisite study, despite significant process variation across sites, almost all resident physicians recalled an adverse event related to the ICU–ward handoff. Future work is needed to determine best practices for ICU–ward handoffs at academic medical centres.

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