mitochondrial cytochrome b
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2024 ◽  
Vol 84 ◽  
Author(s):  
I. Rafaqat ◽  
T. Mahmood ◽  
L. M. Hennelly ◽  
F. Akrim ◽  
I. Uz-Zaman ◽  
...  

Abstract The red fox (Vulpes vulpes) is a medium-sized carnivore that occurs in different regions of Pakistan, however, still lacks scientific data on its ecology and distribution. The current study investigated the phylogenetic status and diet of the red fox (V.v. griffithii) occurring in Ayubia National Park, Pakistan. Through camera trapping and molecular analysis, we confirmed the occurrence of red fox in the study area. Based on mitochondrial cytochrome B (304 bp) and limited sampling, nearly all red foxes of Ayubia National Park and surrounding Himalayan ranges fall within Holarctic maternal lineage, whereas red foxes found in plains of Pakistan are part of the basal Palearctic maternal lineage. Using 32 scats, we found that red fox diet comprises of 80% animal-based prey species (both wild and domestic) and 19% plant matter. The wild animal prey species included Cape hare (Lepus capensis) and flying squirrel (Pteromyini sp.), which constituted 17% and 15% of diet, respectively. Red foxes infrequently consumed House mouse (Mus musculus), Himalayan Palm civet (Paguma larvata) and sheep (Ovis aries), each comprising around 6% to 9% of red fox diet. The fox species also scavenged on domestic donkey opportunistically. Based on our sampling, our study suggests that the red fox (V.v. griffithii) that occurs in Ayubia National Park and across the lesser Himalayan ranges belongs to Holarctic maternal lineage. The study also highlights consumption of plant seeds by red foxes, indicating it may play an important ecological role in seed dispersal in Ayubia National Park.


Biologia ◽  
2021 ◽  
Author(s):  
Tanja Plieger ◽  
Matthias Wolf

AbstractProtothecosis is an infectious disease caused by organisms currently classified within the green algal genus Prototheca. The disease can manifest as cutaneous lesions, olecranon bursitis or disseminated or systemic infections in both immunocompetent and immunosuppressed patients. Concerning diagnostics, taxonomic validity is important. Prototheca, closely related to the Chlorella species complex, is known to be polyphyletic, branching with Auxenochlorella and Helicosporidium. The phylogeny of Prototheca was discussed and revisited several times in the last decade; new species have been described. Phylogenetic analyses were performed using ribosomal DNA (rDNA) and partial mitochondrial cytochrome b (cytb) sequence data. In this work we use Internal Transcribed Spacer 2 (ITS2) as well as 18S rDNA data. However, for the first time, we reconstruct phylogenetic relationships of Prototheca using primary sequence and RNA secondary structure information simultaneously, a concept shown to increase robustness and accuracy of phylogenetic tree estimation. Using encoded sequence-structure data, Neighbor-Joining, Maximum-Parsimony and Maximum-Likelihood methods yielded well-supported trees in agreement with other trees calculated on rDNA; but differ in several aspects from trees using cytb as a phylogenetic marker. ITS2 secondary structures of Prototheca sequences are in agreement with the well-known common core structure of eukaryotes but show unusual differences in their helix lengths. An elongation of the fourth helix of some species seems to have occurred independently in the course of evolution.


Plant Disease ◽  
2021 ◽  
Author(s):  
Marcus Vinicius Marin ◽  
Teresa E Seijo ◽  
Ellias Zuchelli ◽  
Natalia A. Peres

Phytophthora cactorum and P. nicotianae cause leather rot (LR) of fruit and Phytophthora crown rot (PhCR) in strawberry. LR occurs sporadically but can cause up to 70% fruit loss when weather is conducive. In Florida's annual strawberry winter production system, PhCR can be severe, resulting in plant stunting, mortality, and severe yield loss. Currently, azoxystrobin is labeled for control of LR but not for PhCR. The aims of this research were i) to determine the sensitivity of P. cactorum and P. nicotianae isolates from strawberry to azoxystrobin and ii) to investigate mechanisms of QoI-resistance present in P. cactorum and P. nicotianae based on the known point mutations within the cytb gene. Isolates of both Phytophthora spp. causing LR and PhCR were collected from multiple strawberry fields in Florida between 1997 and 2020. Isolates were tested for sensitivity to azoxystrobin at 0, 0.01, 0.1, 1.0, 10, and 50 µg/ml on potato dextrose agar (PDA) amended with SHAM (100 µg/ml). Isolates were separated into two groups, sensitive isolates, with the 50% effective concentration (EC50) values lower than 1.0 µg/ml, and resistant isolates having EC50 values higher than 50 µg/ml. P. cactorum and P. nicotianae resistance to azoxystrobin was found for isolates collected after 2010. The first 450 nucleotides of the mitochondrial cytochrome b (cytb) gene were sequenced from a selection of resistant and sensitive isolates of both species. The G143A mutation reported to confer resistance to azoxystrobin was found in all resistant P. cactorum isolates. However, in P. nicotianae, qualitative resistance was observed, but the isolates lacked all the known mutations in the cytb gene. This is the first report of resistance to azoxystrobin in P. cactorum and P. nicotianae.


2021 ◽  
Vol 67 (4) ◽  
pp. 403-415
Author(s):  
Tu Ngoc Ly ◽  
Son Truong Nguyen ◽  
Masaharu Motokawa ◽  
Duong Thuy Vu ◽  
Hai Tuan Bui ◽  
...  

We found distinct pelage characters in Finlayson’s squirrel (Callosciurus finlaysonii) population, which is endemic to Lao Island of the Cham Islands, located off the coast of central Vietnam. Among squirrels of the ‘C. erythraeus-finlaysonii complex’, which consists of all forms of C. erythraeus and C. finlaysonii, mitochondrial cytochrome-b sequences show that the Lao Island squirrel forms a cluster with C. finlaysonii with external characters of C. erythraeus flavimanus, defined previously as ‘C. finlaysonii morpha flavimanus’. Both squirrel forms, however, differed in pelage colour. This different colouration may have arisen from the effect of geographic isolation.


2021 ◽  
Author(s):  
Yize Guan ◽  
Nan Li ◽  
Tancheng Li ◽  
Liyuan Sun ◽  
Li Ming Cheng

Abstract Bovine bone marrow is traditionally regarded as a highly nutritious food that has been widely used as a medicinal and healthy food for several decades in China. A large number of adulterated and counterfeit bone marrows from pigs and donkeys have been used in place of bovine bone marrow in commercial products, which are almost identical morphologically to species. Therefore, we explored a feasibility of fingerprinting of multiplex PCR gels combined with imaged SDS-PAGE gels of proteins. Three pairs of specific primers for bovine, pig and donkey were designed according to the conserved sequence in mitochondrial cytochrome b. The optimal reaction conditions for triple PCR were optimized. A modified method was used to extract total proteins and SDS-PAGE gels of proteins were set up. A three-fold PCR detection assay was successfully established to identify three species of bovine, pig and donkey. Three primers have good specificity and high sensitivity. Additionally, the assay sensitivity test confirmed that the extracted DNA concentration was the lowest of bovine bone marrow at 0.1 pg. The assay also showed 100% specificity. The electrophoretogram of SDS-PAGE showed distinct electrophoresis profiles among three species. The established fingerprint of multiplex PCR DNA gels combined with imaged SDS-PAGE gels of proteins has strong specificity and can be quickly and accurately used for the identification of bovine bone marrow. Rapid authentication of bovine bone marrow and differentiation from non-bovine products can be achieved using an improved SDS alkali denaturation method, species-specific PCR assay combined with imaged SDS-PAGE gels of proteins.


2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Alexander A. Zamyatnin ◽  
Tatiana A. Belozerskaya ◽  
Andrey A. Zamyatnin

Prior to this study, we discovered a protein characterized by many different amino acid sequences with the same number of amino acid residues. This turned out to be a unique cytochrome b, in which 1048 molecules out of 1689 contain 379 amino acid residues. A detailed study of the occurrence of this protein in living organisms at different taxonomic levels (from biological domains to biological orders of animals) has been carried out in the work presented here. We found that the main part of all b cytochromes is present in eukaryotes (99.2%), in biological kingdoms (95.9% in animals), in biological phylums (97.5% in chordates), and in biological classes (79.7% in mammals). Withal, this protein, containing 379 amino acid residues and characterized by many different amino acid sequences, is found only in eukaryotes (100%), only in animals (100%) and mainly in mammals (81.1%). Thus, a representative that has cytochrome b with a corresponding number of amino acid residues has not yet been identified among archaea and prokaryotes, while it is common in representatives of different biological types, classes, and orders of animals. It is believed that the structural diversity of a given protein within the same length and its one function of participation in the process of electron transfer relate to the physicochemical features of the extra- and intramembrane fragments of the polypeptide chain of this protein.


2021 ◽  
Vol 55 (6) ◽  
pp. 558-565
Author(s):  
Jafar Razeghi ◽  
Peyman Ahmadi Pishtab ◽  
Paria Fathi ◽  
Bahman Panahi ◽  
Mohammad Amin Hejazi

Foods ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2631
Author(s):  
Yu-Min Lee ◽  
Shinyoung Lee ◽  
Hae-Yeong Kim

With an increased consumption of seafood products, food fraud with fish resources has been continuously reported. In particular, codfish has been exploited worldwide as a processed product in fresh, frozen, smoked, canned, or ready-to-eat dish forms. However, it is challenging to identify processed fish products after processing because of their similar morphological characteristics. Substitution and mislabeling of codfish among different species are also happening deliberately or unintentionally. Thus, it is necessary to distinguish cod species to prevent fish adulteration and food fraud. In this study, we developed a multiplex PCR for simultaneously identifying five cod species within Gadidae using capillary electrophoresis. Then, their species-specific primer sets were designed by targeting the mitochondrial cytochrome b gene. Subsequently, the amplicon sizes obtained were 237 bp, 204 bp, 164 bp, 138 bp, and 98 bp for Atlantic cod, Pacific cod, blue whiting, haddock, and Alaska pollock, respectively. The specificity of each primer was further tested using 19 fish species, and no cross-reactivity was observed. The limit of detection of this multiplex PCR assay was 1 pg. The developed multiplex PCR assay can be applied to 40 commercial food products successfully. This detection method will be efficient for managing seafood authentication by simultaneously analyzing multiple cod species.


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