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Mitochondrial validation

Yannic Nonnenmacher, Roberta Palorini, Karsten Hiller
In this chapter, we present an experimental protocol for the targeted metabolic profiling of full cells and mitochondria in selectively permeabilized cells. Mitochondria of adherent cell cultures are made accessible by the addition of digitonin-a compound that selectively permeabilizes the cytosolic membrane without affecting mitochondrial integrity. The generated in situ mitochondria are subsequently used in a stable isotope labeling assay in which their metabolic fluxes can be analyzed without any interfering influence originating from cytosolic components...
2019: Methods in Molecular Biology
Marcelo KovaČiĆ, Sergey V Bogorodsky, Ahmad O Mal, Tilman J Alpermann
The gobiid genus Koumansetta Whitley, placed in synonymy by some authors with the similar genus Amblygobius Bleeker, is redescribed and its validity based on an integrated morphological and molecular assessment is confirmed. The following characters have been found that distinguish Koumansetta from any of 15 recognized valid species of Amblygobius: oculoscapular transverse rows trp and tra long, extending dorsally well above level of rows x1 and x2; snout pointed, prominent, longer than eye diameter, with gently sloping dorsal profile, overhanging mouth; mouth subterminal; the upper limb of first gill arch with 1-2 slender, weak and soft gill rakers anteriorly, followed by 1-5 short, also soft, broad structures; first two dorsal-fin spines elongate, remaining spines progressively shorter; pelvic frenum absent; body brown to brown-green in upper and lateral sides with narrow yellow or orange longitudinal stripes on body and head, black ocellated spot on the second dorsal fin, and another black spot dorsoposteriorly on caudal peduncle...
August 15, 2018: Zootaxa
Pablo Teta, J Pablo Jayat, Cecilia Lanzone, Agustina Ojeda
The leaf-eared mice of the genus Phyllotis (Cricetidae, Phyllotini) encompasses at least 20 species of medium-sized Neotropical rodents mostly distributed throughout the Andean region. Its limits and contents were reviewed by several authors, based both on morphological and molecular data. However, no integrative approaches were conducted based on large samples of individuals with a wide geographical coverage. The purposes of this paper are: (i) to evaluate species limits; and (ii) to test the congruence between molecular and quantitative morphological evidences within the Phyllotis xanthopygus complex in southern South America...
July 16, 2018: Zootaxa
Bianca laÍs Zimmermann, Ivanklin Soares Campos-Filho, Giovanna Monticelli Cardoso, Sandro Santos, JosÉ otÁvio Aguiar, Paula Beatriz Araujo
The use of molecular data in association with classical taxonomy has helped to alleviate the taxonomic impediment through the discovery, delimitation and description of new species. Terrestrial isopods are the largest suborder of Isopoda; however, there are very few active taxonomists in this group and a representative part of the terrestrial isopods world diversity remains unexplored. The genus Atlantoscia comprises five species in which diagnostic characters are few and show subtle differences among the species...
September 19, 2018: Zootaxa
Hiranya Sudasinghe, R H Tharindu Ranasinghe, Sampath de Alwis Goonatilake, Madhava Meegaskumbura
The taxonomy of the three native taxa assigned to the genus Labeo (L. dussumieri, L. fisheri and L. porcellus lankae) in Sri Lanka is reviewed. The population hitherto identified as L. dussumieri in Sri Lanka is shown to be a distinct species, here named L. heladiva. Labeo heladiva, new species, has a wide distribution in the low and mid-elevations of the island and is distinguished from its Indian congeners by the combination of having two pairs of barbels; 12-13 branched dorsal-fin rays; lateral line with 44-51 scales; ½8-½9+1+6-7 scales in transverse series; and 19-22 circumpeduncular scales...
September 28, 2018: Zootaxa
Tomasz W Pyrcz, Jadwiga Lorenc-Brudecka, Pierre Boyer, Anna Zubek
The validity of the monobasic neotropical butterfly genus Cheimas Thieme (Nymphalidae, Satyrinae, Satyrini, Pronophilina) is discussed, and confirmed based on morphological and molecular data. Cheimas opalinus (Staudinger), endemic to the Venezuelan Cordillera de Mérida, and considered prior to this study to be monotypic and restricted to the central part of the range, is demonstrated to be polytypic and more widely distributed. Five subspecies are recognised, differing mostly in their dorsal patterns, in particular the shape and colour of hindwing greenish-blue patch...
May 23, 2018: Zootaxa
Hans Fery, Ignacio Ribera
The subtribe Deronectina Galewski, 1994 (Dytiscidae, Hydroporinae, Hydroporini) is distributed in the Nearctic, in the north of the Neotropical region, and in the Palaearctic and Afrotropical regions. It is currently composed of 194 species and 13 subspecies in eight genera: Amurodytes Fery Petrov, 2013, Boreonectes Angus, 2010, Deronectes Sharp, 1882, Nebrioporus Régimbart, 1906, Oreodytes Seidlitz, 1887, Scarodytes Gozis, 1914, Stictotarsus Zimmermann, 1919, and Trichonectes Guignot, 1941. We present a morphological and a molecular phylogeny of the species of the subtribe, and a revision of their taxonomy to accommodate our phylogenetic results...
September 12, 2018: Zootaxa
Yan-Yan Chen, Rong Li, Chun-Qing Li, Wei-Xian Li, Hong-Fu Yang, Heng Xiao, Shan-Yuan Chen
There are over 60 species within the freshwater fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) distributed throughout the Yunnan-Guizhou Plateau and its surrounding areas in China. In recent years, the increasing number of new species described has raised some controversy about the validity of several species within this genus, notably the putative sympatric species pair S. qiubeiensis and S. jiuchengensis. To test the validity of S. qiubeiensis and S. jiuchengensis, we analyzed the complete sequences of the mitochondrial cytochrome b (CYTB) gene of 20 identified species and one outgroup species...
September 13, 2018: Zootaxa
Xu Li, Wei Zhou
After comparison of the types of the four species of Clupisoma recorded from Yunnan, China, no morphological differences between Clupisoma nujiangense Chen et al. and C. yunnanensis (He, Huang Li) were found, and it is confirmed that the former is a synonym of the latter. Clupisoma yunnanensis occurs in the middle and lower of Nu-jiang, belonging to the Salween River basin. Clupisoma longianale (Huang) and Clupisoma sinense (Huang) are found in the lower Lancang-jiang, in the Mekong River basin. Using concatenated mitochondrial genes and nuclear genes, Wang et al...
September 13, 2018: Zootaxa
C S Stobie, M J Cunningham, C J Oosthuizen, P Bloomer
Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years, however, recent trends focus on genome-wide analyses. One method proposed for calibrating inferences from noisy Next-Generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequences. Most researchers using this approach appear to be unaware that many Single Nucleotide Polymorphisms (SNPs) identified from genome-wide sequence data are themselves mitochondrial, or assume that these are too few to bias analyses...
October 12, 2018: Molecular Ecology Resources
Xiao-Chen Huang, Jin-Hui Su, Jie-Xiu Ouyang, Shan Ouyang, Chun-Hua Zhou, Xiao-Ping Wu
The Yangtze River Basin in China is one of the global hotspots of freshwater mussel (order Unionida) diversity with 68 nominal species. Few studies have tested the validity of these nominal species. Some taxa from the Yangtze unionid fauna have not been adequately examined using molecular data and well-positioned phylogenetically with respect to the global Unionida. We evaluated species boundaries of Chinese freshwater mussels, and disentangled their phylogenetic relationships within the context of the global freshwater mussels based on the multi-locus data and complete mitochondrial genomes...
October 8, 2018: Molecular Phylogenetics and Evolution
S B Barreto, A T Silva, H Batalha-Filho, P R A M Affonso, A M Zanata
An integrative approach based on morphological and multilocus genetic data was used to describe a new species of Nematocharax from the headwaters of the upper Contas River on the Diamantina Plateau, north-eastern Brazil and to infer the relationships among evolutionary lineages within this fish genus. Multispecies coalescent inference using three mitochondrial and five nuclear loci strongly supports a basal split between Nematocharax venustus and the new species, whose distinctive morphological characters include absence of filamentous rays on pelvic fins of maturing and mature males, reduced anal-fin lobe length and lower body depth...
October 10, 2018: Journal of Fish Biology
P Rachitha, K Krupashree, G V Jayashree, Hemanth Kumar Kandikattu, Narayanappa Amruta, Natarajan Gopalan, M K Rao, Farhath Khanum
Herbal medicines are known to mitigate radical induced cell damage. Hence identification and scientific validation of herbal medicines contribute to better use in Ayurvedic/Unani research. In the present study, we investigated antioxidant and anti-apoptotic properties of Convolvulus pluricaulis ( C. pluricaulis ). C. pluricaulis exhibited antioxidant potential evident by free radical scavenging activities. C. pluricaulis pretreatment inhibited H2 O2 induced macromolecule damage such as plasmid DNA damage and AAPH induced oxidation of bovine serum albumin and lipid peroxidation of rat hepatic tissues...
October 2018: Journal of Traditional and Complementary Medicine
Natsumi Maruoka, Hajime Ohtsuki, Wataru Makino, Jotaro Urabe
We examined the morphology of Daphnia individuals maintained in our laboratory for several years, originally collected in Lake Inbanuma, Chiba, Japan. We determined partial sequences of the mitochondrial cytochrome c oxidase subunit I and 12S rRNA genes from specimens in the cultured material. These animals are morphologically similar to D. obtusa Kurz, 1874 , but genetically distinct from this species. Our detailed observation shows that the morphological characteristics in the female and male individuals of our material are highly congruent with those of D...
October 2018: Zoological Science
Takafumi Nakano, Ko Tomikawa
The systematic status of the stygobitic amphipod, Paramoera relicta Uéno, 1971, was revisited based on morphological examination of the paratypes, and molecular phylogenetic analyses using a newly collected specimen from its type locality. The paratypes clearly showed that this species does not possess the "sinusoid" antennal sinus in the head, which was erroneously described in the original description of this species; P. relicta is unquestionably classified within the genus Paramoera Miers, 1875 ...
October 2018: Zoological Science
Carolina Jaquenod De Giusti, Barbara Roman, Samarjit Das
Abnormal mitochondrial calcium ([Ca2+ ]m ) handling and energy deficiency results in cellular dysfunction and cell death. Recent studies suggest that nuclear-encoded microRNAs (miRNA) are able to translocate in to the mitochondrial compartment, and modulate mitochondrial activities, including [Ca2+ ]m uptake. Apart from this subset of miRNAs, there are several miRNAs that have been reported to target genes that play a role in maintaining [Ca2+ ]m levels in the cytoplasm. It is imperative to validate miRNAs that alter [Ca2+ ]m handling, and thereby alter cellular fate...
2018: Frontiers in Physiology
Michelle Levene, Dario Pacitti, Charlotte Gasson, Jamie Hall, Marcia Sellos-Moura, Bridget E Bax
Erythrocyte encapsulated thymidine phosphorylase is recombinant Escherichia coli thymidine phosphorylase encapsulated within human autologous erythrocytes and is under development as an enzyme replacement therapy for the ultra-rare inherited metabolic disorder mitochondrial neurogastrointestinal encephalomyopathy. This study describes the method validation of a two-step bridging electrochemiluminescence immunoassay for the detection of anti-thymidine phosphorylase antibodies in human serum according to current industry practice and regulatory guidelines...
December 14, 2018: Molecular Therapy. Methods & Clinical Development
Alan Diot, Thomas Agnew, Jeremy Sanderson, Chunyan Liao, Janet Carver, Ricardo Pires das Neves, Rajeev Gupta, Yanping Guo, Caroline Waters, Sharon Seto, Matthew J Daniels, Eszter Dombi, Tiffany Lodge, Karl Morten, Suzannah A Williams, Tariq Enver, Francisco J Iborra, Marcela Votruba, Joanna Poulton
Background: Autosomal dominant optic atrophy (ADOA) is usually caused by mutations in the essential gene, OPA1. This encodes a ubiquitous protein involved in mitochondrial dynamics, hence tissue specificity is not understood. Dysregulated mitophagy (mitochondria recycling) is implicated in ADOA, being increased in OPA1 patient fibroblasts. Furthermore, autophagy may be increased in retinal ganglion cells (RGCs) of the OPA1Q285STOP mouse model. Aims: We developed a mouse model for studying mitochondrial dynamics in order to investigate mitophagy in ADOA...
2018: Frontiers in Cell and Developmental Biology
Sarah Zobel, Mechthild Lorenz, Giada Frascaroli, Janik Böhnke, Nicole C Bilz, Megan L Stanifer, Steeve Boulant, Sandra Bergs, Uwe G Liebert, Claudia Claus
Rubella virus (RV) infection impacts cellular metabolic activity in a complex manner with strain-specific nutritional requirements. Here we addressed whether this differential metabolic influence was associated with differences in oxidative stress induction and subsequently with innate immune response activation. The low passaged clinical isolates of RV examined in this study induced oxidative stress as validated through generation of the reactive oxygen species (ROS) cytoplasmic hydrogen peroxide and mitochondrial superoxide...
October 3, 2018: Viruses
E Yilmaz, S Wongkamchai, S Ramünke, G D Koutsovoulos, M L Blaxter, S Poppert, R Schaper, G von Samson-Himmelstjerna, J Krücken
Dirofilaria repens is a zoonotic, mosquito-borne filaria infecting carnivores, particularly dogs. It is expanding its range in Europe but epidemiological information is sparse for other Eurasian regions. In Hong Kong and India, the closely related species Candidatus Dirofilaria hongkongensis was proposed. Previous analysis of 2.5 kb partial mitochondrial genome sequences containing the particularly variable non-coding control region revealed low diversity in European D. repens while Asian nematodes showed high diversity...
October 3, 2018: Transboundary and Emerging Diseases
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