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Background: Scabies, an infestation of the mite Sarcoptes scabiei, has seen an increase in clinical diagnoses in the Netherlands since 2011. This study aimed to analyse PCR-positive S. scabiei skin samples through partial genome sequencing and to link findings to patient epidemiological characteristics. Methods: Skin samples were collected from individuals in the Netherlands between January 2016 and January 2023. On the PCR-positive S. scabiei skin samples, partial mitochondrial cytochrome c oxidase subunit 1 gene (cox1) sequencing was performed to assess genetic variability. Epidemiological information was collected through interviews. We examined associations between cox1 subtypes, epidemiological factors and treatment outcomes. Results: Sequencing results were obtained from 128 patients, with epidemiological information available for 55 (43%) of these patients. Fifteen distinct cox1 subtypes were identified. Subtype 01 was most prevalent (45%) and present across all age groups and social settings. The remaining subtypes were less common and not consistently found in all contexts. Five clusters were identified, each with identical cox1 subtypes. Comparative analysis with GenBank sequences revealed genetic similarities with strains from Australia, the USA and China, suggesting the global distribution and transmission of specific subtypes. A substantial proportion (73%) of patients with scabies required multiple treatments to eradicate the infestation, with no subtype-related differences. Conclusions: This is the first study linking S. scabiei sequencing results to patient epidemiological data. Several subtypes clustered in specific geographic regions and social contexts, underscoring localised transmission patterns. Further research with larger sample sizes is needed to enhance our understanding of the transmission of this mite. This study provides valuable insights that will strengthen scabies control efforts. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA (mtDNA) analysis is a valuable tool in forensic for species identification because mtDNA is maternally inherited, and there are often many copies of mtDNA in a cell. This makes it possible to obtain DNA from degraded or small samples, such as those found in forensic investigations. Additionally, mtDNA analysis can provide information on the evolutionary relationships among different populations and species. In the present study, mtDNA analysis was employed to examine the genetic diversity and phylogenetics of small Blackbuck populations in Haryana, India. The six tissue and eleven fecal samples were collected and amplified with the cytochrome c oxidase subunit I gene. Various statistical approaches were used to examine the parameters like Genetic p-distance, Genetic diversity, Tajima's D, Fu's Fs Test, Mismatch distribution graphs. The overall value of p = 0.013 and Hd = 0.65 of all selected populations suggested that the population of Blackbuck under investigation may have an equilibrium stage. The findings of present investigation provide insight into the genetic diversity and highlight the importance of maintaining connectivity among fragmented populations. This information is crucial for designing effective conservation strategies, as well as for addressing issues associated with species identification and combating wildlife-related crimes. [ABSTRACT FROM AUTHOR]

The Calotes genus presents a challenge due to the complexity of its species. However, research on the cryptic species complex within the Indonesian Calotes genus is still lacking. This study aims to determine the extent of genetic relationships and assess the potential existence of a species complex within the Indonesian genus Calotes (Daudin, 1802) (Squamata, Agamidae) using the partial Cytochrome c Oxidase Subunit 1 (COI) gene sequence as a molecular marker. Samples of the Indonesian Calotes genus in this study were collected from South Lampung (Lampung), Bogor (West Java), and Langkat (North Sumatra). By aligning 582 bp sequence similarities with reference sequences in GenBank, we confirmed that seven out of eight samples analyzed belonged to Calotes vultuosus, while one sample was identified as Calotes versicolor. The identity values ranged from 96 to 100%. The C. vultuosus samples in this study displayed lower genetic distances, ranging from 0 to 3%, with the reference C. vultuosus sequence from Indonesia compared to the reference sequence from India, which ranged from 6 to 9%. Phylogenetic tree reconstruction, utilizing both maximum likelihood with IQ-Tree and Bayesian Inference with BEAST methods, further supports these findings. It reveals distinct groupings between C. vultuosus samples from Indonesia and India. These results suggest the potential occurrence of a species complex within the Indonesian genus Calotes. Furthermore, the inclusion of eight COI gene sequences from two Calotes species in the GenBank database has the potential to confirm the existence of previously undocumented species in Indonesia. [ABSTRACT FROM AUTHOR]

Cytochrome c (CytC), a one-electron carrier, transfers electrons from complex bc1 to cytochrome c oxidase (CcO) in the electron-transport chain. Electrostatic interaction with the partners, complex bc1 and CcO, is ensured by a lysine cluster near the heme forming the Universal Binding Site (UBS). We constructed three mutant variants of mitochondrial CytC with one (2Mut), four (5Mut), and five (8Mut) Lys->Glu substitutions in the UBS and some compensating Glu->Lys substitutions at the periphery of the UBS for charge compensation. All mutants showed a 4–6 times increased peroxidase activity and accelerated binding of cyanide to the ferric heme of CytC. In contrast, decomposition of the cyanide complex with ferrous CytC, as monitored by magnetic circular dichroism spectroscopy, was slower in mutants compared to WT. Molecular dynamic simulations revealed the increase in the fluctuations of Cα atoms of individual residues of mutant CytC compared to WT, especially in the Ω-loop (70–85), which can cause destabilization of the Fe...S(Met80) coordination link, facilitation of the binding of exogenous ligands cyanide and peroxide, and an increase in peroxidase activity. It was found that only one substitution K72E is enough to induce all these changes, indicating the significance of K72 and the Ω-loop (70–85) for the structure and physiology of mitochondrial CytC. In this work, we also propose using a ferro-ferricyanide buffer as a substrate to monitor the peroxidase activity of CytC. This new approach allows us to determine the rate of peroxidase activity at moderate (200 µM) concentrations of H2O2 and avoid complications of radical formation during the reaction. [ABSTRACT FROM AUTHOR]

Specimen identification at the species level is a critical challenge for understanding community structure and conserving biodiversity. The use of mitochondrial DNA barcodes, in addition to morphology, has proven to be a useful tool for earthworm identification, but it has also raised difficulties. Thus, approaches to delineating molecular operational taxonomic units (MOTUs) from cytochrome c oxidase subunit 1 (COI) or 16S rDNA sequence data often reveal more mitochondrial lineages than morphospecies, raising the question of whether these MOTUs should be used as taxonomic entities in community structure studies. Here, we used a newly acquired dataset of 576 COI barcodes of earthworms from Metropolitan France that were clustered in 36 MOTUS, corresponding to 21 morphospecies. We also incorporated data gathered from the literature to investigate this question. In order to match our MOTUs with already-described mitochondrial lineages, we downloaded reference sequences from the GenBank and BOLD platforms. In light of the difficulties encountered in recovering these sequences, we recommend that any new mitochondrial lineage described in a study be named consistently with previous works. Next, we analyzed the biological, ecological, and molecular data available in the literature on the different mitochondrial lineages that matched our MOTUs in order to determine if there was a consensus for species delimitation. Although the study specimens mainly belong to the Lumbricidae, which is one of the most studied families of earthworms, the data are often missing to determine if the MOTUs correspond to different species. Pending revision of the taxonomy, MOTUs for which mitochondrial divergence has been confirmed by morphological differences should be considered distinct taxonomic entities in community structure studies. In the absence of morphological differences and pending more data, we propose to distinguish for these analyses, within sexually reproducing morphospecies, the MOTUs for which mitochondrial divergence has been confirmed by multilocus nuclear data, while in the case of reproduction by parthenogenesis, ecological differences between MOTUs are necessary to consider them as different taxonomic entities. [ABSTRACT FROM AUTHOR]

Species of the catfish genus Rineloricaria are common in the Paraíba do Sul River basin, in southeastern Brazil; here we present a revision of the taxonomic diversity and geographic distribution of the species of the genus inhabiting the basin, based on novel morphologic and molecular data. Five species delimitation methods based on cytochrome C oxidase subunit 1 nucleotide sequences yielded comparable molecular operational taxonomic units. The automatic barcode gap discovery, assemble species by automatic partitioning, barcode index number, and Bayesian implementation of the Poisson tree process methods supported the recognition of five evolutionary lineages. These taxonomic units were assigned to the previously described Rineloricaria nigricauda, Rineloricaria steindachneri, Rineloricaria zawadzkii, and Rineloricaria nudipectoris, and an additional undescribed species. R. zawadzkii was further divided into two intraspecific geographically structured lineages using the generalized mixed Yule coalescent delimitation method. A maximum likelihood phylogenetic analysis revealed that the five lineages from the Paraíba do Sul have closer relationships to different species from southern and southeastern Brazil (Ribeira de Iguape, Lagoa dos Patos, Uruguay, Paraguay, and Parana river basins) than to each other. Based on the analysis of lectotypes, recently collected material, and specimens from ichthyological collections, the poorly described R. nigricauda and R. steindachneri are redescribed following current descriptive standards. The undescribed species from the middle and upper Paraíba do Sul River basin is formally described. The description of a new species, along with the description of species boundaries in R. nigricauda and R. steindachneri, contributes to the knowledge of the ichthyofauna of the Paraíba do Sul River basin and adjacent coastal drainages of southeastern Brazil. An identification key for the species of Rineloricaria occurring in the Paraíba do Sul River basin is provided. [ABSTRACT FROM AUTHOR]

Cymoxanil (CYM) is a widely used synthetic acetamide fungicide, but its biochemical mode of action remains elusive. Since CYM inhibits cell growth, biomass production, and respiration in Saccharomyces cerevisiae, we used this model to characterize the effect of CYM on mitochondria. We found it inhibits oxygen consumption in both whole cells and isolated mitochondria, specifically inhibiting cytochrome c oxidase (CcO) activity during oxidative phosphorylation. Based on molecular docking, we propose that CYM blocks the interaction of cytochrome c with CcO, hampering electron transfer and inhibiting CcO catalytic activity. Although other targets cannot be excluded, our data offer valuable insights into the mode of action of CYM that will be instrumental in driving informed management of the use of this fungicide. [ABSTRACT FROM AUTHOR]

The coastal marine stingrays (genus Fontitrygon) include two endemic and highly threatened species (Fontitrygon margaritella and Fontitrygon margarita) from the African Gulf of Guinea. However, the lack of robust diagnostic features due to similar external features hinders species identification, thus limiting species‐specific conservation efforts.The present study aims to examine the morphological characteristics and apply a DNA barcoding tool through amplifying mitochondrial cytochrome C oxidase subunit I (mtCOI) to accurately identify F. margaritella and F. margarita from coastal waters in Nigeria, Cameroon, Côte d'Ivoire, Guinea Bissau and Senegal.Morphological evaluation revealed differences in colour pattern, eye shade, mouth shape and pectoral radial count between F. margarita and F. margaritella. We generated 25 mtCOI barcode sequences that included F. margaritella (n = 22) and F. margarita (n = 3). Our query search in the National Center for Biotechnology Information (NCBI) GenBank and Barcode of Life Data system (BOLD) showed a sequence match of our newly collected F. margaritella with other F. margaritella in the global databases, while mtCOI sequences of F. margarita were new to the NCBI GenBank and BOLD databases. The phylogenetic clustering analyses based on the maximum‐likelihood tree grouped morphospecies into highly supported monophyletic units.Our study demonstrates the potential of combined molecular and morphological approaches in the identification of coastal marine stingrays from the Gulf of Guinea. Our study is helpful in future scientific studies and in forming future conservation plans. [ABSTRACT FROM AUTHOR]

Molecular methods are currently some of the best-suited technologies for implementation in insect monitoring. However, the field is developing rapidly and lacks agreement on methodology or community standards. To apply DNA-based methods in large-scale monitoring, and to gain insight across commensurate data, we need easy-to-implement standards that improve data comparability. Here, we provide three recommendations for how to improve and harmonize efforts in biodiversity assessment and monitoring via metabarcoding: (i) we should adopt the use of synthetic spike-ins, which will act as positive controls and internal standards; (ii) we should consider using several markers through a multiplex polymerase chain reaction (PCR) approach; and (iii) we should commit to the publication and transparency of all protocol-associated metadata in a standardized fashion. For (i), we provide a ready-to-use recipe for synthetic cytochrome c oxidase spike-ins, which enable between-sample comparisons. For (ii), we propose two gene regions for the implementation of multiplex PCR approaches, thereby achieving a more comprehensive community description. For (iii), we offer guidelines for transparent and unified reporting of field, wet-laboratory and dry-laboratory procedures, as a key to making comparisons between studies. Together, we feel that these three advances will result in joint quality and calibration standards rather than the current laboratory-specific proof of concepts. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'. [ABSTRACT FROM AUTHOR]

Cytochrome c (Cytc) is important for both mitochondrial respiration and apoptosis, both of which are altered in cancer cells that switch to Warburg metabolism and manage to evade apoptosis. We earlier reported that lysine 53 (K53) of Cytc is acetylated in prostate cancer. K53 is conserved in mammals that is known to be essential for binding to cytochrome c oxidase and apoptosis protease activating factor-1 (Apaf-1). Here we report the effects of this acetylation on the main functions of cytochrome c by expressing acetylmimetic K53Q in cytochrome c double knockout cells. Other cytochrome c variants analyzed were wild-type, K53R as a control that maintains the positive charge, and K53I, which is present in some non-mammalian species. Intact cells expressing K53Q cytochrome c showed 49% decreased mitochondrial respiration and a concomitant increase in glycolytic activity (Warburg effect). Furthermore, mitochondrial membrane potential was decreased, correlating with notably reduced basal mitochondrial superoxide levels and decreased cell death upon challenge with H2O2 or staurosporine. To test for markers of cancer aggressiveness and invasiveness, cells were grown in 3D spheroid culture. K53Q cytochrome c-expressing cells showed profoundly increased protrusions compared to WT, suggesting increased invasiveness. We propose that K53 acetylation of cytochrome c is an adaptive response that mediates prostate cancer metabolic reprogramming and evasion of apoptosis, which are two hallmarks of cancer, to better promote tumor survival and metastasis. [ABSTRACT FROM AUTHOR]

Estimating parasitism rates in the field is essential for developing and evaluating biocontrol strategies using parasitoids. In this study, we developed a simple polymerase chain reaction (PCR)‐based method for detecting parasitism of the cassava mealybug Phenacoccus manihoti Matile‐Ferrero (Hemiptera: Pseudococcidae) by the primary parasitoid Anagyrus lopezi De Santis (Hymenoptera: Encyrtidae) and its hyperparasitoid Prochiloneurus pulchellus Silvestri (Hymenoptera: Encyrtidae). Primers were designed to amplify partial cytochrome c oxidase subunit I genes of each species, and their sensitivity was evaluated with mealybugs that had been parasitized by A. lopezi 0, 3, and 6 days earlier, and mummified mealybugs containing A. lopezi pupae that had been parasitized by P. pulchellus 0, 3, 6, 9, and 12 days earlier. The detection rate of parasitism by A. lopezi was 100% for all ages of A. lopezi. The detection rate of parasitism by P. pulchellus ranged from 94.1% to 100%, depending on its developmental stage. For P. pulchellus, template DNA was diluted 10 times before PCR because PCR with the original concentration showed low detection rates, presumably due to the presence of PCR inhibitors. Overall, our primers can be considered sufficiently sensitive to be used for detecting each species. [ABSTRACT FROM AUTHOR]

The sole known heme enzyme of the parasitic protist Giardia intestinalis is a flavohemoglobin (gFlHb) that acts as a nitric oxide dioxygenase (NOD) and protects the organism from the free radical nitric oxide. To learn more about the properties of this enzyme, we measured its nitric oxide dioxygenase, NADH oxidase, and cytochrome c reductase activities and compared these to the activities of the E. coli flavohemoglobin (Hmp). The turnover number for the NOD activity of gFlHb (23 s−1) is about two-thirds of that of Hmp (34 s−1) at pH 6.5 and 37 °C. The two enzymes differ in their sensitivity towards molecules that act as heme ligands. For both gFlHb and Hmp, inhibition with miconazole, a large imidazole ligand, is adequately described by simple competitive inhibition, with KI = 10 μM and 0.27 μM for gFlHb and Hmp, respectively. Inhibition plots with the small ligand imidazole were biphasic, which is consistent with previous experiments with carbon monoxide as a probe that show that the active site of flavohemoglobins exists in two conformations. Interestingly, the largest difference is observed with nitrite, which, like imidazole, also shows a biphasic inhibition plot; however, nitrite inhibits gFlHb at sub-millimolar concentrations while Hmp is not significantly affected. NADH oxidase activity measured under aerobic conditions in the absence of nitric oxide for Hmp was more than twice the activity of gFlHb. The addition of 1 mM hydrogen peroxide in these assays stimulated the NADH oxidase activity of gFlHb but not Hmp. Both enzymes had nearly identical cytochrome c reductase activities but the extent of the contribution of indirect reduction by flavohemoglobin-generated superoxide was much lower with gFlHb (4% SOD-inhibited) than with Hmp (17% SOD-inhibited). Although the active sites of the two enzymes share the same highly conserved residues that are important for catalysis, differences in the distal ligand binding site may account for these differences in activity and sensitivity towards NOD inhibitors. The differences observed in the NADH oxidase and cytochrome c reductase assays suggest that gFlHb may have evolved to protect the protist, which lacks both superoxide dismutase and catalase, from the damaging effects of superoxide by minimizing its production and from peroxide by actively reducing it. [ABSTRACT FROM AUTHOR]

Iriomote Island is a small continental island hosting approximately 40 rivers characterized by short, steep-gradient streams and small waterfalls. We examined the population genetic structure and diversity of the freshwater prawn Macrobrachium shokitai Fujino & Baba, 1973 (Palaemonidae) using the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence. Specimens were collected from 19 sites along ten rivers on the island, covering the known geographic distribution of the species. Haplotype and nucleotide diversities were very low within each river on the island. Nearly all haplotypes were exclusive to a given river, confirming distinct population structures among rivers at a small geographical scale. Slight genetic differentiation was discerned between the upper and lower sites of waterfalls in only the Yuchin River. Phylogenetic tree reconstruction, haplotype network, and principle coordinate analysis classified five clades roughly correspond to geographical groups in the western, southern, central, and northern regions of the island. Extreme caution should therefore be taken when translocating individuals to other rivers to avoid introducing genetic disturbance, even during conservation and mitigation efforts. [ABSTRACT FROM AUTHOR]

Purines are the building blocks of DNA/RNA, energy substrates, and cofactors. Purine metabolites, including ATP, GTP, NADH, and coenzyme A, are essential molecules in diverse biological processes such as energy metabolism, signal transduction, and enzyme activity. When purine levels increase, excess purines are either recycled to synthesize purine metabolites or catabolized to the end product uric acid. Purine catabolism increases during states of low oxygen tension (hypoxia and ischemia), but this metabolic pathway is incompletely understood in the context of histotoxic hypoxia (i.e., inhibition of oxygen utilization despite normal oxygen tension). In rabbits exposed to cyanide—a classical histotoxic hypoxia agent—we demonstrated significant increases in several concordant metabolites in the purine catabolic pathway (including plasma levels of uric acid, xanthosine, xanthine, hypoxanthine, and inosine) via mass spectrometry-based metabolite profiling. Pharmacological inhibition of the purine catabolic pathway with oxypurinol mitigated the deleterious effects of cyanide on skeletal muscle cytochrome c oxidase redox state, measured by non-invasive diffuse optical spectroscopy. Finally, plasma uric acid levels correlated strongly with those of lactic acid, an established clinical biomarker of cyanide exposure, in addition to a tissue biomarker of cyanide exposure (skeletal muscle cytochrome c oxidase redox state). Cumulatively, these findings not only shed light on the in vivo role(s) of cyanide but also have implications in the field of medical countermeasure (MCM) development. [ABSTRACT FROM AUTHOR]

Despite is known to have widespread distribution and the most active species of the family Chlorocyphidae, the molecular data of Rhinocypha fenestrella (Rambur, 1842) are relatively scarce. The present study is the first that examined the genetic diversity and phylogeographic pattern of the peacock jewel-damselfly R. fenestrella by sequencing the cytochrome C oxidase I (cox1) and 16S rRNA gene regions from 147 individuals representing eight populations in Malaysia. A total of 26 and 10 unique haplotypes were revealed by the cox1 and 16S rRNA genes, respectively, and 32 haplotypes were recovered by the concatenated sequences of cox1+16S. Analyses indicated that haplotype AB2 was the most frequent and the most widespread haplotype in Malaysia while haplotype AB1 was suggested as the common ancestor haplotype of the R. fenestrella that may arose from the Negeri Sembilan as discovered from cox1+16S haplotype network analysis. Overall haplotype and nucleotide diversities of the concatenated sequences were Hd = 0.8937 and Pi = 0.0028, respectively, with great genetic differentiation (FST = 0.6387) and low gene flow (Nm = 0.14). Population from Pahang presented the highest genetic diversity (Hd = 0.8889, Pi = 0.0022, Nh = 9), whereas Kedah population demonstrated the lowest diversity (Hd = 0.2842, Pi = 0.0003, Nh = 4). The concatenated sequences of cox1+16S showed genetic divergence ranging from 0.09% to 0.97%, whereas the genetic divergence for cox1 and 16S rRNA genes were 0.16% to 1.63% and 0.01% to 0.75% respectively. This study provides for the first-time insights on the intraspecific genetic diversity, phylogeographic pattern and ancestral haplotype of Rhinocypha fenestrella. The understanding of molecular data especially phylogeographic pattern can enhance the knowledge about insect origin, their diversity, and capability to disperse in particular environments. [ABSTRACT FROM AUTHOR]

Three new species of the genera Thiania C. L. Koch, 1846 and Yaginumaella Prószyński, 1979 are described and named as T. bamian sp. nov. (♂♀), T. flacata sp. nov. (♀) and Y. curvata sp. nov. (♂♀), from Hunan Province, China. Detailed descriptions, photos of somatic features and copulatory organs, as well as a distribution map are provided. Nucleotide data for the barcoding gene, cytochrome c oxidase subunit I (COI) of T. bamian sp. nov. (♂♀) and Y. curvata sp. nov. (♀) are provided. [ABSTRACT FROM AUTHOR]

A new species, Diacyclops dyabdar sp. nov. from the Diacyclops crassicaudis (Sars, 1863) species group from northern Middle Siberia, is described. This species is interesting from an ecological point of view, as it lives mainly in watercourses. It is well-distinguished from other species of the group by the presence of spinules on the first segments of the third and fourth pairs of swimming legs, details of the ornamentation on the fourth pair of legs and caudal rami. A detailed comparison of the new species and D. crassicaudis is presented. Molecular markers, including cytochrome c oxidase (COI) of mtDNA and 18S rRNA, ITS1 and ITS2 of nuclear DNA were obtained for a single female of D. dyabdar sp. nov. A morphometric analysis of species and subspecies of the D. crassicaudis group was carried out. It showed slight differences between the described subspecies and some species. On this basis, the subspecies D. crassicaudis, as well as D. iranicus Pesce & Maggi, 1982 and D. fontinalis Naidenow, 1969, are synonymized with the subspecies type. A more precise diagnosis of the D. crassicaudis group is indicated. This group now includes six species. The taxonomic position of several questionable taxa of Diacyclops Kiefer, 1927 described from Iran is discussed: D. landei Mahoon & Zia, 1985; D. bicuspidatus jurenei Najam-un-Nisa, Mahoon & Irfan Khan, 1987; D. landei richardi Parveen, Mahoon & Saleem, 1988 and D. jurenei Parveen, Mahoon & Saleem, 1988. These taxa are accepted as nomen dubium. [ABSTRACT FROM AUTHOR]

In this paper, a new genus in the nudibranch family Discodorididae, Avaldesia n. gen. is established for Avaldesia albomacula (Chan & Gosliner, 2007) and Avaldesia tahala (Chan & Gosliner, 2007), originally assigned to the genus Thordisa Bergh, 1877, and a new species, Avaldesia tamatoa n. sp. described here from the central Pacific. To establish species relationships within Avaldesia , as well as the placement of Avaldesia within Discodorididae, we utilized four molecular markers (cytochrome c oxidase subunit I, 16S rRNA, histone H3 and 28S rRNA) in our Bayesian inference and maximum likelihood analyses. Four species delimitation methods were complemented by morphological dissections and scanning electron microscopy. Our results reveal a clear separation between Avaldesia and Thordisa and suggest that Avaldesia is more closely related to the genera Hoplodoris Bergh, 1880 and Asteronotus Ehrenberg, 1831. The most characteristic features of Avaldesia include a radula with increasing denticulation towards the fimbriate outermost laterals and a reproductive system with a lobate vestibular gland, occasional hollow vestibular spine and a penis armed with one or more penial spines. All species of Avaldesia are found in shallow water (5–10 m depth) on rocky reefs, sandy sediments and algal fields with distributions across the Indo-Pacific. [ABSTRACT FROM AUTHOR]

In Mycobacterium smegmatis, the transcriptional activity of the alternative sigma factor SigF is posttranslationally regulated by the partner switching system consisting of SigF, the anti-SigF RsbW1, and three anti-SigF antagonists (RsfA, RsfB, and RsbW3). We previously demonstrated that expression of the SigF regulon is strongly induced in the Δaa3 mutant of M. smegmatis lacking the aa3 cytochrome c oxidase, the major terminal oxidase in the respiratory electron transport chain. Here, we identified and characterized the RsfSR twocomponent system involved in regulating the phosphorylation state of the major anti-SigF antagonist RsfB. RsfS (MSMEG_6130) is a histidine kinase with the cyclase/histidine kinase-associated sensing extracellular 3 domain at its N terminus, and RsfR (MSMEG_6131) is a receiver domain-containing protein phosphatase 2C-type phosphatase that can dephosphorylate phosphorylated RsfB. We demonstrated that phosphorylation of RsfR on Asp74 by RsfS reduces the phosphatase activity of RsfR toward phosphorylated RsfB and that the cellular abundance of the active unphosphorylated RsfB is increased in the Δaa3 mutant relative to the WT strain. We also demonstrated that the RsfSR two-component system is required for induction of the SigF regulon under respirationinhibitory conditions such as inactivation of the cytochrome bcc1 complex and aa3 cytochrome c oxidase, as well as hypoxia, electron donor-limiting, high ionic strength, and low pH conditions. Collectively, our results reveal a key regulatory element involved in regulating the SigF signaling system by monitoring the state of the respiratory electron transport chain. [ABSTRACT FROM AUTHOR]

Purpose: The aim of this study is to conduct a molecular characterization of Spirometra tapeworm from jungle cat (Felis chaus) in Guilan Province, north of Iran using DNA sequence analysis of the mitochondrial cytochrome c oxidase subunit 1 (Cox1) and 12S rDNA sequences. Methods: Morphological features of the adult tapeworm of Spirometra were evaluated using specific staining and light microscopy. The molecular characterization was performed using partial Cox1 and 12S rDNA regions. Genetic diversity was calculated and phylogenetic trees of the obtained sequences were constructed. Results: Morphological features were compatible with previous description of adult Spirometra erinaceieuropaei. The Cox1 sequence of the specimen showed 100% similarity with S. erinaceieuropaei sequences in GenBank from Korea, China and Iran. Also, the 12S rDNA sequence revealed 99.7% similarity with S. erinaceieuropaei isolates from China and Japan. Intra-species variation within isolates of S. erinaceieuropaei was 0–1.4% and 0–4.6% for Cox1 and 12S rDNA genes, respectively. Conclusion: This is the first report of molecular characterization of S. erinaceieuropaei in jungle cat, F. chaus in Iran. Jungle cat probably plays a major role as reservoir host in maintaining of this parasite in this area with favorable climate condition. Needs for further assessment on the role of appropriate hosts, especially intermediate/paratenic hosts as well as the potential risk of human infectivity with sparganosis is emphasized. [ABSTRACT FROM AUTHOR]

Purpose: Derogenes ruber Lühe, 1900, the type-species of the genus Derogenes Lühe, 1900, is a poorly known derogenid digenean. The original description of this species was not illustrated and aspects of the morphology of the parasite from the type-host remain scarce. Available records of this species were brief and/or lacked illustrations and were based on morphology alone. Additionally, molecular data for Derogenes spp. are warranted to untangle species complexes as they provide a better assessment of interspecific genetic divergence. Methods: Derogenes ruber is redescribed based on newly collected specimens from the gall bladder of its type-host Chelidonichthys lastoviza (Bonnaterre, 1788) collected in the Western Mediterranean off the Algerian coast during 2017–2019 and molecular data are provided using a partial fragment of the nuclear 28S ribosomal RNA gene (28S rRNA), the internal transcribed spacer 2 (ITS2) and a fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. Results: We herein provide a detailed illustrated redescription and morphometric data of D. ruber from its type-host C. lastoviza. We report a new geographical record (off Algeria) for it. Derogenes ruber is also genetically characterised for the first time. Species/lineages of Derogenes were recovered in five strongly supported reciprocally monophyletic clades: (i) D. ruber from C. lastoviza off Algeria; (ii) D. lacustris from Galaxias maculatus (Jenyns) off Argentina; (iii) Lineage "D. varicus DV1" (D. varicus sensu stricto) from fish hosts in the White and Barents seas and the North Sea; (iv) Lineage "D. varicus DV2" from mollusc hosts in the White Sea; and (v) Lineage "D. varicus DV3" from Eumicrotremus fedorovi Mandrytsa. in the Pacific Ocean. Hence, comparison of the newly generated sequences with other available data for Derogenes species supports the distinction of D. ruber confirming its taxonomic status and helping assess interspecific variation. Comparison of D. ruber with the closely related species Derogenes latus revealed overlaps in morphometric data and the validity of the latter species is questioned. Conclusion: The combination of morphological and molecular data provided for D. ruber provides a firm foundation for further investigations of Derogenes spp. Although we do describe herein material of D. ruber from the type-host, given that the occurrence of a single Derogenes species in various hosts has been challenged by molecular data, and both D. lacustris and D. varicus sensu stricto had been genetically proven to occur in various hosts, D. ruber and D. latus may be indeed synonymous. Additional sequencing effort on Derogenes spp. will strengthen systematic comparative studies and evolutionary relationships within the Derogenidae in general. [ABSTRACT FROM AUTHOR]

The dispersal mode of estuarine invertebrates has a strong effect on genetic variability and phenotypic expression, potentially maintaining gene flow among widely separated populations or limiting connectivity among close ones. Understanding the dispersal strategies effects can support adequate strategies for environment management and understand the evolutionary history of the studied species. A comparative study on the effect of larval dispersal strategies (export vs retention) along the overall geographic distribution ranges of adult populations of two co‐distributed fiddler crab species was performed. Geometric morphometric techniques were used to evaluate morphological differentiation in the shape of the carapace and major cheliped propodus in 10 populations of Minuca mordax and five populations of Leptuca leptodactyla. Potential genetic differentiation was assessed using DNA sequence data from up to 170 fiddler crab specimens, corresponding to the mitochondrial gene cytochrome c oxidase subunit 1 (COX1). Patterns of genetic and morphological characteristics diverged among populations of both species. In terms of morphology, populations of both species showed intraspecific variation in the shape of the carapace and, to a lesser extent, in the major cheliped propodus. This observed intraspecific variation followed a clear geographic pattern of morphometric differentiation, in which the geographic origin is associated with a phenotypic response to the environmental diversity along the extended Brazilian coast. In contrast, there are shared haplotypes in populations separated by more than 4000 km, but with significant ΦST values among most populations of L. leptodactyla and M. mordax, suggesting a moderate to high level of gene flow. Therefore, it can be concluded that the split of the Central South Equatorial Current has not acted as an efficient long‐term barrier to the dispersal of larvae in both species. In M. mordax, a slight limitation of genetic exchange can be observed between the southernmost populations and the remaining ones. This first evidence of genetic structuring within this widely distributed species is consistent with its documented strategy to retain larvae in the estuarine environments. However, occasional transport of larvae to more open coastal waters seems to maintain stepwise gene flow between neighboring populations. Overall, our results still provide evidence of more pronounced genetic homogeneity in a species with a larval export strategy (L. leptodactyla) compared to a species with a larval retention strategy (M. mordax). This suggests that larval dispersal strategies, coupled with the microhabitat in which the respective species occur, have a noticeable effect on the degree of gene flow. Most likely, these biological aspects are further influenced by the estuarine and coastline geomorphology. [ABSTRACT FROM AUTHOR]

Genetic screens have been used extensively to probe interactions between nuclear genes and their impact on phenotypes. Probing interactions between mitochondrial genes and their phenotypic outcome, however, has not been possible due to a lack of tools to map the responsible polymorphisms. Here, using a toolkit we previously established in Drosophila, we isolate over 300 recombinant mitochondrial genomes and map a naturally occurring polymorphism at the cytochrome c oxidase III residue 109 (CoIII109) that fully rescues the lethality and other defects associated with a point mutation in cytochrome c oxidase I (CoIT300I). Through lipidomics profiling, biochemical assays and phenotypic analyses, we show that the CoIII109 polymorphism modulates cardiolipin binding to prevent complex IV instability caused by the CoIT300I mutation. This study demonstrates the feasibility of genetic interaction screens in animal mitochondrial DNA. It unwraps the complex intra-genomic interplays underlying disorders linked to mitochondrial DNA and how they influence disease expression. Chiang et al. map a genetic interaction in animal mitochondrial DNA by recombination. This reveals how polymorphisms in two complex IV subunits jointly affect cardiolipin binding to impact complex stability, organismal fitness and disease expression. [ABSTRACT FROM AUTHOR]

The terminal oxidases of bacterial aerobic respiratory chains are redox-active electrogenic enzymes that catalyze the four-electron reduction of O2 to 2H2O taking out electrons from quinol or cytochrome c. Living bacteria often deal with carbon monoxide (CO) which can act as both a signaling molecule and a poison. Bacterial terminal oxidases contain hemes; therefore, they are potential targets for CO. However, our knowledge of this issue is limited and contradictory. Here, we investigated the effect of CO on the cell growth and aerobic respiration of three different Escherichia coli mutants, each expressing only one terminal quinol oxidase: cytochrome bd-I, cytochrome bd-II, or cytochrome bo3. We found that following the addition of CO to bd-I-only cells, a minimal effect on growth was observed, whereas the growth of both bd-II-only and bo3-only strains was severely impaired. Consistently, the degree of resistance of aerobic respiration of bd-I-only cells to CO is high, as opposed to high CO sensitivity displayed by bd-II-only and bo3-only cells consuming O2. Such a difference between the oxidases in sensitivity to CO was also observed with isolated membranes of the mutants. Accordingly, O2 consumption of wild-type cells showed relatively low CO sensitivity under conditions favoring the expression of a bd-type oxidase. [ABSTRACT FROM AUTHOR]

The genomes of species belonging to the genus Colletotrichum harbor a substantial number of cytochrome P450 monooxygenases (CYPs) encoded by a broad diversity of gene families. However, the biological role of their CYP complement (CYPome) has not been elucidated. Here, we investigated the putative evolutionary scenarios that occurred during the evolution of the CYPome belonging to the Colletotrichum Graminicola species complex (s.c.) and their biological implications. The study revealed that most of the CYPome gene families belonging to the Graminicola s.c. experienced gene contractions. The reductive evolution resulted in species restricted CYPs are predominant in each CYPome of members from the Graminicola s.c., whereas only 18 families are absolutely conserved among these species. However, members of CYP families displayed a notably different phylogenetic relationship at the tertiary structure level, suggesting a putative convergent evolution scenario. Most of the CYP enzymes of the Graminicola s.c. share redundant functions in secondary metabolite biosynthesis and xenobiotic metabolism. Hence, this current work suggests that the presence of a broad CYPome in the genus Colletotrichum plays a critical role in the optimization of the colonization capability and virulence. [ABSTRACT FROM AUTHOR]

With 74 genera and subgenera and approximately 740 species, Saprininae represent one of the largest subfamilies of Histeridae (Coleoptera: Histeroidea). Here, we present a phylogenetic hypothesis for Saprininae based on comprehensive taxonomic sampling. This is the first phylogenetic study combining molecular and morphological approaches (cytochrome c oxidase subunit 1, 18S ribosomal RNA and 93 morphological characters). As a result, we propose a new classification; five new tribes are erected: Myrmetini Portevin stat. and sens. nov.; Euspilotini Lackner, trib. nov.; Eremosaprinini Lackner, trib. nov.; Saprinini Blanchard, sens. nov.; and Hypocaccini Lackner, trib. nov. Additional nomenclatural acts are as follows: Chelyoxenus Hubbard is downgraded to a subgenus of Geomysaprinus Ross, thus Geomysaprinus (Chelyoxenus) stat. nov., Nessus Reichardt is transferred from a subgenus of Hypocaccus C. Thomson to a subgenus of Hypocacculus Bickhardt, thus Hypocacculus (Nessus) stat. rest. The following taxa Paraphilothis Vienna, Styphrus Motschulsky, Xerosaprinus Wenzel, Lophobregmus Wenzel, Vastosaprinus Wenzel, Auchmosaprinus Wenzel, Hemisaprinus Kryzhanovskij & Reichardt, Reichardtia Wenzel and Australopachylopus Lackner & Leschen are all downgraded into subgenera of Saprinus Erichson. Thus, Saprinus (Paraphilothis) stat. nov., Saprinus (Styphrus) stat. nov., Saprinus (Xerosaprinus) stat. nov., Saprinus (Vastosaprinus) stat. nov., Saprinus (Auchmosaprinus) stat. nov., Saprinus (Lophobregmus) stat. nov., Saprinus (Hemisaprinus) stat. rest., Saprinus (Reichardtia) stat. nov., Saprinus (Australopachylopus) stat. nov. A new genus, Paraxenus Lackner gen. nov., is proposed for the former South African and Namibian members of the genus Pholioxenus Reichardt, with the following new combinations: Paraxenus diasi (Vienna) comb. nov.; Paraxenus eremicola (Thérond) comb. nov.; Paraxenus namibiensis (Vienna) comb. nov.; Paraxenus oleolus (Thérond) comb. nov.; Paraxenus therondi (Olexa) comb. nov.; and Paraxenus uhligi (Mazur) comb. nov. Additionally, based on the analysis of the dispersal patterns, Myrmetini appear to be a bipolar (amphitropical) clade, while Eremosaprinini appear to be exclusive to the Western Hemisphere. Euspilotini are strongly represented in the Western Hemisphere, with only a handful of species known from the Palaearctic/Oriental regions. Saprinini and Hypocaccini are spread worldwide but are poorly represented in South America. The Holarctic (in particular the Nearctic) Region is proposed as the centre of origin of the subfamily around 80 million years ago (Ma). Inquilinism is hypothesised to be the ancestral state for the group, with several subsequent independent shifts in life histories. Saprininae cladogenesis occurred mainly during the Palaeogene (66–23.03 Ma) and could be linked to the diversification of mammals. [ABSTRACT FROM AUTHOR]

Available DNA barcodes of freshwater zooplankton are scarce in regions like the Iberian Peninsula, which harbours many rare and endemic species and is considered a hotspot of crustacean biodiversity. Recently, a new species of Ceriodaphnia (Cladocera: Daphniidae) was described using morphological analysis of specimens in the Mediterranean region and molecular data on a single locality in southern Spain. In our study, we detected the presence of the newly discovered taxa and here, we provide new DNA sequences on the barcoding region mitochondrial cytochrome c oxidase I together with ecological information of the recently described Ceriodaphnia smirnovi. Additionally, we built a molecular phylogenetic tree and genetically compared these specimens with previously available mitochondrial DNA sequences and with new sequences of the genus recovered in Iberia. Our data suggest that this morphospecies might contain some cryptic taxa and might be more common than previously thought, occupying temporary to semi‐permanent ecosystems, with vegetation and highly variable pH and turbidity conditions. Moreover, the existence of a non‐identified clade within our phylogenetic tree requires additional morphological research. Our study highlights the need for further research on microcrustacean biota to better constrain its spatial boundaries, phylogenetic relationship and determine species hiding cryptic diversity. [ABSTRACT FROM AUTHOR]

DNA metabarcoding requires reference libraries that link DNA sequences to species. Mitochondrial gene regions cytochrome c oxidase I (COI), 12S ribosomal RNA (12S rRNA), 16S ribosomal RNA (16S rRNA), cytochrome b (cyt b) and the hypervariable control region (D-loop) are routinely used in studies that measure genetic diversity in animal species. This study aimed to review the state of DNA reference libraries for small South African mammals as small mammals constitute a large portion of small and medium carnivore diet. Analyses of DNA records revealed that of 193 small mammal species in South Africa, only 141 have DNA sequences available for one or more of the mitochondrial genes examined. Cyt b had the highest species coverage, with 59.1% of South African species represented in the reference libraries. COI only has 33.7%, 12S rRNA has 23.8%, D-loop has 17.6%, and 16S rRNA has the lowest species coverage of 15%. This study supports the use of multiple gene regions when performing scat metabarcoding, particularly when wanting to determine the small mammal component of the diet. Additionally, it emphasises the need to build comprehensive DNA reference libraries linking sequences to taxonomically identified species. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the quantitative relationships between four fish species from three genera based on molecular analyses (barcoding) of nine species from five genera utilizing the mitochondrial COI gene. Species within the same genus showed more transitional incompatibilities than transversional mismatches. The samples were divided into four main groups by a phylogenetic tree built from the sequencing data (cytochrome COI) of samples from the two populations using the neighbour-joining method. As dissimilar species were clustered under separate nodes and similar species were clustered under the same nodes, the neighbour-joining tree revealed various clusters corresponding to the taxonomic status of the species. In conclusion, the mitochondrial CO1 gene is a useful molecular marker for DNA barcoding. [ABSTRACT FROM AUTHOR]

The Coccinellidae is a highly diversified family of order Coleoptera. Coccinellid ladybirds are well known for their role as biological control agent against varied range of agricultural pests. The samples of coccinellid ladybird collected from Pakistan were identified and characterized as Micraspis allardi (Mulsant, 1866). This is one of the least-studied ladybird species with limited work on its ecological distribution as a biological control agent. The genus Micraspis has vast genetic diversity with a possible presence of unknown number of cryptic species. Sequence information of some species of the genus Micraspis are present in NCBI database. However, least molecular data or sequences describing M. allardi could be available from database. Therefore, morphological and molecular characterization was imperative for this species. Here, the samples collected from sugarcane field of Faisalabad District of Pakistan and were identified by using morphological and molecular protocols. For molecular identification, two different regions of mitochondrial cytochrome c oxidase I (COI) gene (COI-5′ and COI- 3′) were used as molecular markers for the identification of the species. Morphological appearance, DNA sequence similarity searches and phylogenetic analysis collectively indicated it as M. allardi. To the best of our knowledge, this is the first report providing molecular evidence of M. allardi using mitochondrial DNA barcode region (658bp) as well as mtCOI-3ʹ sequences (817bp). The study will help in understanding population genetics through diversity analysis, ecological role, and phenotypic structures associated with the geographic range of this species. [ABSTRACT FROM AUTHOR]

Background: Non-small cell lung cancer (NSCLC) is a major pathological type of lung cancer. However, its pathogenesis remains largely unclear. MRPL35 is a regulatory subunit of the mitoribosome, which can regulate the assembly of cytochrome c oxidases and plays an important role in the occurrence of NSCLC. Methods: The expression of MRPL35 in NSCLC was detected by tissue microarray and immunohistochemistry. H1299 cells were infected with lentivirus to knockdown MRPL35, and the cells were subjected to crystal violet staining to assess the results of colony formation assays. A549 cells were infected by lentiviral particles-expressing shMRPL35 or shControl, and then subcutaneously injected into nude mice. Tumorigenesis in mice was detected by in vivo imaging. The potential pathway of MRPL35 in NSCLC was assessed by Western blotting. Results: MRPL35 was over-expressed in NSCLC tissue compared to para-cancerous and normal tissues. Knockdown of MRPL35 suppressed cell proliferation and decreased NSCLC progression both in vitro and in vivo. The possible molecular mechanisms were also clarified, which indicated that MRPL35 could be involved in cell apoptosis and proliferation by modulating the expression levels of CDK1, BIRC5, CHEK1, STMN1 and MCM2. Knockdown of MRPL35 activated p53 signaling pathway and inhibited cell cycle regulation. Conclusions: The oncogenic role of MRPL35 in NSCLC was potentially mediated through the cell cycle regulatory genes such as BIRC5, STMN1, CDK1, CHEK1 and MCM2, as well as activation of P53 signaling pathway. [ABSTRACT FROM AUTHOR]

Syllinae is the largest and the most diverse subfamily in Syllidae and usually a dominant group in many marine habitats, both in terms of numbers of species and individuals. However, the lack of morphological synapomorphies for many genera and the non-monophyly of most of these suggested by molecular studies, have stressed taxonomic and systematic problems within this subfamily. Although several studies have revised some genera in the Indo-Pacific area, important gaps of knowledge remain for this biogeographic region. Thus, in this study we undertook detailed morphological examination of Syllis and Megasyllis specimens from the Philippine Islands and provide a phylogenetic analysis of Indo-Pacific Syllinae in order to evaluate the position of newly described species. We provide line drawings, light microscopy observations and electron microscopy micrographs for eight species, including five new to science. Maximum likelihood and Bayesian inference analyses of four molecular markers (28S rRNA, 18S rRNA, 16S rRNA, cytochrome c oxidase subunit I) from 85 specimens are presented, showing the non-monophyletic status of Syllis and Megasyllis. Overall, our study increases the biodiversity of syllids in this poorly known Indo-Pacific area, highlighting the importance of examining both morphological and molecular data to expand our knowledge of the subfamily Syllinae and to further resolve the taxonomic issues that remain in this group. The following new taxa are described: Megasyllis kurui sp. nov. Moreno-Martínez, San Martín & Álvarez-Campos, Syllis ireneae sp. nov. Moreno-Martínez, San Martín & Álvarez-Campos, Syllis santii sp. nov. Moreno-Martínez, San Martín & Álvarez-Campos, Syllis tini sp. nov. Moreno-Martínez, Syllis walong sp. nov. Moreno-Martínez, San Martín & Álvarez-Campos. [ABSTRACT FROM AUTHOR]

The white-eared opossum, Didelphis albiventris Lund, 1840, is one of the most widely distributed South American marsupials. As currently defined, the species ranges from northeastern and central Brazil through Paraguay and central Bolivia, all of Uruguay, and in Argentina, from the north to northern Patagonia. Previous phylogeographic analyses found two haplogroups, one corresponding to northeastern and central Brazil and the other to southern Brazil, Bolivia, and Paraguay. In those studies, differentiation was based on the geographic distance between both regions and the presence of geographic barriers among populations. The aims of the present contribution were to perform population-genetic analyses using the mitochondrial markers cytochrome c oxidase 1 (COI) and cytochrome b (cyt b) in order to elucidate the phylogeographic history of this species by incorporating samples from Argentina into the published datasets, and to evaluate whether there is more than one taxonomic entity under the name Didelphis albiventris. We studied the craniodental morphology of the species and used environmental niche modeling (ENM) as an additional methodology to investigate the environmental factors affecting its distribution. Our molecular, morphological, and ENM results strongly suggest the existence of two taxonomic entities under Didelphis albiventris, one in southern Brazil, Argentina, Paraguay, Uruguay, and Bolivia, and the other in central and northern Brazil. Data from specimens in the missing middle part of the taxon's range and evidence from nuclear markers are needed before formalizing a taxonomic split. [ABSTRACT FROM AUTHOR]

Molecular examination of representatives of Balaustium from several populations in SW Poland, performed using the sequence data from the mitochondrial cytochrome c oxidase subunit I, confirmed their common specific affiliation and identity with Balaustium murorum. The potential presence of distinct species in the studied material, preliminarily inferred from the discovery of clusters as a result of Principal Component Analysis exploring the metric data sets, was rejected due to the finding of only one haplotype, at intra- and inter-population sampling. An insight into meristic traits in larvae, focused on chaetotaxy of legs, revealed wider variation than hitherto recognized for the species. The variation was higher in laboratory-reared larvae compared to field-collected ones. The overall deviations from the mean character values at intra- and interpopulation levels, higher than hitherto observed for the species, vote for the reappraisal of the criteria adopted for discrimination of members of Balaustium with the application of an integrative approach. [ABSTRACT FROM AUTHOR]

Background: Soil microbial fuel cells (MFCs) can remove antibiotics and antibiotic resistance genes (ARGs) simultaneously, but their removal mechanism is unclear. In this study, metagenomic analysis was employed to reveal the functional genes involved in degradation, electron transfer and the nitrogen cycle in the soil MFC. Results: The results showed that the soil MFC effectively removed tetracycline in the overlapping area of the cathode and anode, which was 64% higher than that of the control. The ARGs abundance increased by 14% after tetracycline was added (54% of the amplified ARGs belonged to efflux pump genes), while the abundance decreased by 17% in the soil MFC. Five potential degraders of tetracycline were identified, especially the species Phenylobacterium zucineum, which could secrete the 4-hydroxyacetophenone monooxygenase encoded by EC 1.14.13.84 to catalyse deacylation or decarboxylation. Bacillus, Geobacter, Anaerolinea, Gemmatirosa kalamazoonesis and Steroidobacter denitrificans since ubiquinone reductase (encoded by EC 1.6.5.3), succinate dehydrogenase (EC 1.3.5.1), Coenzyme Q-cytochrome c reductase (EC 1.10.2.2), cytochrome-c oxidase (EC 1.9.3.1) and electron transfer flavoprotein-ubiquinone oxidoreductase (EC 1.5.5.1) served as complexes I, II, III, IV and ubiquinone, respectively, to accelerate electron transfer. Additionally, nitrogen metabolism-related gene abundance increased by 16% to support the microbial efficacy in the soil MFC, and especially EC 1.7.5.1, and coding the mutual conversion between nitrite and nitrate was obviously improved. Conclusions: The soil MFC promoted functional bacterial growth, increased functional gene abundance (including nitrogen cycling, electron transfer, and biodegradation), and facilitated antibiotic and ARG removal. Therefore, soil MFCs have expansive prospects in the remediation of antibiotic-contaminated soil. This study provides insight into the biodegradation mechanism at the gene level in soil bioelectrochemical remediation. [ABSTRACT FROM AUTHOR]

Two Cerrado rust fungi, Phakopsora rossmaniae and Aplopsora hennenii, described in 1993 and 1995 and originally assigned to families Phakopsoraceae and Ochropsoraceae, respectively, were subjected to molecular phylogenetic analyses using fragments of the nuc 28S and 18S rDNA and mitochondrial cytochrome c oxidase subunit 3 (CO3) gene. Although both taxa were morphologically well placed in their original genera, they were shown to belong in a strongly supported new lineage within the Raveneliineae distant from the Phakopsoraceae and Ochropsoraceae. Therefore, we properly treated this lineage as the new genus Cerradopsora now harboring C. rossmaniae (type species) and C. hennenii. However, this novel phakopsoroid genus remains in uncertain familial position without support to be included in any of the families that share space within the Raveneliineae. [ABSTRACT FROM AUTHOR]

Background: Deer heart is a valuable traditional Chinese medicinal material. At present, there is no functional component or symbol component for deer heart, and it is difficult to identify them by physical and chemical methods. In this study, we established deer heart identification method based on mtDNA cytb gene, and developed a deer heart DNA detection kit. Results: There were specific amplification bands in reference medicinal materials and true deer hearts at 194 bp, but no amplification bands in negative control and blank control. Deer heart DNA detection kit has good specificity, reproducibility and stability, and its sensitivity can reach 0.5 mg. Conclusions: The application of the deer heart DNA detection kit is simple and easy to operate, and the results obtained using the kit is stable, which is suitable for popularization and application. [ABSTRACT FROM AUTHOR]

During the past decade, the ca 120 species of small, colourful tropical Asian freshwater fishes previously referred to the cyprinid genus Puntius have been shown to consist of multiple morphologically distinct evolutionary lineages that resolve as monophyletic groups in molecular studies. Many of these clades have been allocated to new genera such as Dawkinsia, Desmopuntius, Haludaria, Oliotius, Pethia, Puntigrus, Sahyadria, Striuntius and Waikhomia. Others have been assigned to existing but previously poorly delineated genera such as Barbodes and Systomus, while some 40 species remain in Puntius. The divergent morphology of several species retained in Puntius suggests, however, that the systematics of this group requires further attention. Here, based on a phylogeny incorporating newly generated data from the mitochondrial cytochrome b (cytb), mitochondrial cytochrome c oxidase subunit 1 (cox1), nuclear recombination activating protein 1 (rag1), and interphotoreceptor retinoid‐binding protein (irbp) gene markers, we investigate the interrelationships of the species of Puntius in Sri Lanka in the wider context of their Indian and Southeast Asian congeners. We identify three well‐supported monophyletic groups that warrant recognition as new genera: Rohanella (type species Puntius titteya), Plesiopuntius (type species Gnathopogon bimaculatus) and Bhava (type species Puntius vittatus). The first of these is endemic to rainforest streams in Sri Lanka's perhumid southwestern wet zone, whereas the latter two are widely distributed in both Sri Lanka and southern India, including the Western Ghats. Our study highlights the presence of distinct evolutionary lineages among several widespread species. [ABSTRACT FROM AUTHOR]

Charopidae is a highly speciose family of land snails mostly distributed in the main landmasses and archipelagos of the Southern Hemisphere, with a few genera in the Northern Hemisphere. DNA sequencing is making substantial contributions to understanding the phylogeography of Charopidae and the systematic relationships of its subfamilies and related families in the Punctoidea. Here, new data from 28S rRNA are combined with available GenBank sequences to investigate whether Australian Charopidae comprise a single clade, exclusive of species from other regions. Phylogenetic analyses show that this is not the case, with most species from Australia and other regions included in a bootstrap-supported clade that excludes some Australian species. Analyses of concatenated 28S rRNA data and available cytochrome c oxidase subunit I (COI) also contradicted monophyly of Australian species, as did analyses of inferred COI protein sequences. In DNA analyses, the genus Hirasea and Australian taxa with an incomplete secondary ureter were basal within Charopidae. We also examined whether known doubts about the taxonomic status of supra-generic clades in Punctoidea could be resolved by considering autapomorphic COI amino acid changes. Such variation could not generally be applied as an objective criterion for taxonomic categorization but did identify some clades for taxonomic investigation. [ABSTRACT FROM AUTHOR]

Cytochrome c (cyt c) has been suggested as a diagnostic biomarker for non-small cell lung cancer (NSCLC) screening and is a confirmatory method for NSCLC diagnosis. In diagnosed NSCLC patients, the concentration of cyt c in the blood is decreased from the healthy range of ⁓3 nM to about ⁓1 nM. Here, by immobilizing cytochrome oxidase nanoparticles (COxNPs), onto gold nanoparticles (AuNPs) decorated graphene nanosheets (GrNs) modified pencil graphite electrode (PGE), we have constructed a high-resolution electrochemical nanosensor for the detection of the cyt c. The constructed working electrode (AuNPs-GrNs/COxNPs/PGE) was characterized by a scanning electron microscope, energy-dispersive X-ray analysis, and Fourier transform infrared spectroscopy at every stage of its construction. The proposed cyt c nanosensor performed best at optimal pH and temperature of 7.0 and 35o C, respectively, with a maximum potential of 0.317 V. Fabricated cyt c nanosensor showed a wide linear range (0.1 nM–5.1 nM) and low limit of detection (0.136 nM) with satisfactory selectivity, sensitivity (0.93mAcm−2 nM−1), and stability. The proposed approach employed less expensive raw materials to make it successful and most importantly, it is an environment-friendly method. It was successfully employed for detecting cyt c levels in sera samples of NSCLC patients and healthy individuals. [ABSTRACT FROM AUTHOR]

Heme-copper oxygen reductases are membrane-bound oligomeric complexes that are integral to prokaryotic and eukaryotic aerobic respiratory chains. Biogenesis of these enzymes is complex and requires coordinated assembly of the subunits and their cofactors. Some of the components are involved in the acquisition and integration of different heme and copper (Cu) cofactors into these terminal oxygen reductases. As such, MFS-type transporters of the CalT family (e.g., CcoA) are required for Cu import and heme-CuB center biogenesis of the cbb3-type cytochrome c oxidases (cbb3-Cox). However, functionally homologous Cu transporters for similar heme-Cu containing bo3-type quinol oxidases (bo3-Qox) are unknown. Despite the occurrence of multiple MFS-type transporters, orthologs of CcoA are absent in bacteria like Escherichia coli that contain bo3-Qox. In this work, we identified a subset of uncharacterized MFS transporters, based on the presence of putative metal-binding residues, as likely candidates for the missing Cu transporter. Using a genetic approach, we tested whether these transporters are involved in the biogenesis of E. coli bo3-Qox. When respiratory growth is dependent on bo3-Qox, because of deletion of the bd-type Qox enzymes, three candidate genes, yhjE, ydiM, and yfcJ, were found to be critical for E. coli growth. Radioactive metal uptake assays showed that ΔydiM has a slower 64Cu uptake, whereas ΔyhjE accumulates reduced 55Fe in the cell, while no similar uptake defect is associated with ΔycfJ. Phylogenomic analyses suggest plausible roles for the YhjE, YdiM, and YfcJ transporters, and overall findings illustrate the diverse roles that the MFS-type transporters play in cellular metal homeostasis and production of active heme-Cu oxygen reductases. [ABSTRACT FROM AUTHOR]

Heme-copper respiratory oxidases are highly efficient molecular machines. These membrane enzymes catalyze the final step of cellular respiration in eukaryotes and many prokaryotes: the transfer of electrons from cytochromes or quinols to molecular oxygen and oxygen reduction to water. The free energy released in this redox reaction is converted by heme-copper respiratory oxidases into the transmembrane gradient of the electrochemical potential of hydrogen ions ΔμH+). Heme-copper respiratory oxidases have a unique mechanism for generating ΔμH+, namely, a redox-coupled proton pump. A combination of direct electrometric method for measuring the kinetics of membrane potential generation with the methods of prestationary kinetics and site-directed mutagenesis in the studies of heme-copper oxidases allows to obtain a unique information on the translocation of protons inside the proteins in real time. The review summarizes the data of studies employing time-resolved electrometry to decipher the mechanisms of functioning of these important bioenergetic enzymes. [ABSTRACT FROM AUTHOR]

Two species of thrips, Rhipiphorothrips concoloratus Zhang and Tong and Trichromothrips antidesmae Li, Li and Zhang, under the family Thripidae are recorded new to India. The diagnostic characters of both the species are discussed. In addition, Euphysothrips minozzii Bagnall of the family Thripidae is redescribed with illustrations based on the specimens collected on an agriculturally important new host plant, Groundnut. The hypothesis of E. minozzii being associated with fungus is discussed. The partial sequence data of mitochondrial cytochrome c oxidase (mtCOI) for E. minozzii is generated and submitted to the Barcode of Life Data System (BOLD). The generated barcode sequence of the species is a novel contribution in global database. [ABSTRACT FROM AUTHOR]

Phenazines are heteroaromatic compounds consisting of a central pyrazine ring fused with two benzenes. Different functional groups attached to the dibenzopyrasin core cause differences in the chemical, physical, and biological properties of phenazines. Interest in these compounds has not diminished for decades. New biological activities and practical applications discovered in recent years force researchers to investigate all aspects of the synthesis, degradation, and mechanisms of action of phenazines. In this study, we have demonstrated the involvement of the coxA gene product (cytochrome c oxidase, su I) in the production of phenazines in P. chlororaphis subsp. aurantiaca. Overlap PCR was used to knock out the coxA gene and the resulting mutants were screened for their ability to grow on rich and minimal culture media and for phenazine production. The reintroduction of the full-length coxA gene into the B-162/coxA strains was used to further confirm the role of this gene product in the ability to produce phenazines. We were able to show that the product of the coxA gene is necessary for phenazine production in rich growth media. At the same time, the CoxA protein does not seem to have any effect on phenazine production in M9 minimal salt medium. We could show that knocking down even one subunit of the cytochrome c oxidase complex leads to a significant reduction (to trace concentrations) or complete suppression of phenazine antibiotic production on rich PCA medium in P. chlororaphis subsp. aurantiaca. [ABSTRACT FROM AUTHOR]

Sarcocystis spp. infects water buffaloes (Bubalus bubalis) causing sarcocystosis. In the present study, Sarcocystis fusiformis was recognized in Egyptian water buffaloes based on histological observation and molecular analysis of internal transcribed spacer 1 (ITS1), 18S ribosomal RNA (18S rRNA) and cytochrome c oxidase subunit I (COX-1) gene fragments. Chemotherapy and vaccines against Sarcocystis spp. could potentially target proteases because they may play a crucial role in the infection. Cysteine proteases are multifunctional enzymes involved in vital metabolic processes. However, the involvement of proteases in S. fusiform infection has not yet been characterized. Here, the purification and study on some biochemical properties of protease isolated from cysts of S. fusiform were carried out. Protease with a molecular weight of 100 kDa was purified. LC–MS/MS analyzed the protein sequence of purified protease and the data suggested that the enzyme might be related to the cysteine protease. The purified protease exhibited maximum activity at pH 6 and a temperature of 50 °C. The Michaelis–Menten constant (Km), the maximum velocity (Vmax), and the turnover number (Kcat) were determined. The complete inhibition effect of cysteine inhibitors indicated that the purified enzyme is a cysteine protease. The results suggested that S. fusiform proteolytic enzyme may be necessary for parasite survival in water buffaloes by digesting host tissues. Therefore, cysteine protease could be a suitable target for vaccinations. [ABSTRACT FROM AUTHOR]

Gorals represent ungulate mammals of the Palearctic and Indo-Malayan realms that face habitat destruction and intense hunting pressure. Their classification has been the subject of various (mainly genetic) assessments in the last decade, but some results are conflicting, hampering some conservation-based decisions. Genetic sampling of gorals has increased considerably in recent years, at least for mitochondrial (mt) DNA. Results based on two mt genes (cytochrome b and the D-loop) are currently available. Still, the utility of cytochrome oxidase subunit I remains unanalysed, even though it belongs among the gene markers that enable a correct species identification in mammals. This study examines phylogenetic relationships and species delimitation in gorals using all currently available cytochrome oxidase subunit I sequences, including the not yet analysed goral population from Pakistan. Our results of various phylogenetic approaches, such as maximum parsimony, likelihood and Bayesian inference, and exploration of species boundaries via species delimitation support the validity of six species of goral, namely N. baileyi, N. caudatus, N. cranbrooki, N. evansi, N. goral, and N. griseus. This result accords well with results based on other mt genes, especially the cytochrome b from the highly exhaustive data sampling. Our study also summarises common sources of errors in the assessment of goral phylogeny and taxonomy and highlights future priorities in understanding goral diversification. [ABSTRACT FROM AUTHOR]

All known photosynthetic cyanobacteria carry a cytochrome c6 protein that acts transferring electrons from cytochrome b6f complex to photosystem I, in photosynthesis, or cytochrome c oxidase, in respiration. In most of the cyanobacteria, at least one homologue to cytochrome c6 is found, the socalled cytochrome c6B or cytochrome c6C. However, the function of these cytochrome c6-like proteins is still unknown. Recently, it has been proposed a common origin of these proteins as well as the reclassification of the cytochrome c6C group as c6B, renaming the new joint group as cytochrome c6BC. Another homologue to cytochrome c6 has not been classified yet, the formerly called cytochrome c6-3, which is present in the heterocyst-forming filamentous cyanobacteria Nostoc sp. PCC 7119. In this work, we propose the inclusion of this group as an independent group in the genealogy of cytochrome c6-like proteins with significant differences from cytochrome c6 and cytochrome c6BC, with the proposed name cytochrome c6D. To support this proposal, new data about phylogeny, genome localisation and functional properties of cytochrome c6-like proteins is provided. Also, we have analysed the interaction of cytochrome c6-like proteins with cytochrome f by isothermal titration calorimetry and by molecular docking, concluding that c6-like proteins could interact with cytochrome b6f complex in a similar fashion as cytochrome c6. Finally, we have analysed the reactivity of cytochrome c6-like proteins with membranes enriched in terminal oxidases of cyanobacteria by oxygen uptake experiments, concluding that cytochrome c6D is able to react with the specific copper-oxidase of the heterocysts, the cytochrome c oxidase 2. [ABSTRACT FROM AUTHOR]

There are several factors, such as genetic drift, gene flow and migration that affect the population genetic structure and phylogeographic distribution of genetic lineages within single species. Previous studies of the bladder grasshoppers, Bullacris unicolor of South Africa, showed divergence in mitochondrial CO1 (cytochrome c oxidase subunit 1) haplotype diversity and significant genetic structure. In this study, we revisit these findings adding more samples from different locations and using mitochondrial CO1 and Internal transcribed spacer (ITS) gene sequences. We tested the hypothesis that the western, northern and eastern distribution ranges of B. unicolor show different population genetic patterns, corresponding with isolation-by-distance. Mitochondrial CO1 and ITS data were collected for 99 individuals from 12 localities across the Western, Northern and Eastern sides of South Africa. Overall, significant variation in genetic structure was found across the localities as indicated by FST analyses. Haplotype and phylogeographical analyses suggested that restricted gene flow played a role in shaping current genetic patterns, although isolation-by-distance was not supported, as confirmed by Mantel tests. Phylogenetic trees of both genetic sequences revealed two major clades, with western and northern sides. Also, the major clades exhibit a few sub-clades within the localities, showing other factors shaping the genetic structure of B. unicolor include the geographical barriers, and most likely due to changes in habitat specificity and habitat fragmentation. Taken together, this study aims to contribute information on the population structure and genetic diversity of B. unicolor populations across South Africa. [ABSTRACT FROM AUTHOR]

Hydatigera taeniaeformis is a cestode that uses felines and rodents as definitive and intermediate hosts, respectively. Its larval stage, or metacestode, infects a wide variety of rodent species and develops in the liver parenchyma into a cyst. The aim of this study was to evaluate the occurrence of H. taeniaeformis metacestode in various species of wild rodents from Peru. For this, the livers of 356 rodents were macroscopically examined for any parasitic form compatible with metacestodes. Metacestodes were identified by measuring characteristic morphological parameters, and the diagnosis was confirmed by molecular analysis of a fragment of the cytochrome c oxidase subunit 1 gene (cox1). Five rodents: two small-eared pygmy rice rats (Oligoryzomys microtis), two white-naped squirrels (Simosciurus nebouxii), and one pygmy rice rat (Oligoryzomys sp.) were infected with H. taeniaeformis metacestodes. The cox1 sequences from our metacestodes showed up to 100% identity with previous H. taeniaeformis sequences from the GenBank. These results demonstrated the occurrence of H. taeniaeformis in new intermediate hosts, as well as the first molecular contribution for H. taeniaeformis from Peru. [ABSTRACT FROM AUTHOR]