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Growth hormone (GH) modifies liver gene transcription in a sexually dimorphic manner to meet liver metabolic demands related to sex; thus, GH dysregulation leads to sex-biased hepatic disease. We dissected the steps of the GH regulatory cascade modifying GH-dependent genes involved in metabolism, focusing on the male-predominant genes Lcn13 , Asns , and Cyp7b1 , and the female-predominant genes Hao2 , Pgc1a , Hamp2 , Cyp2a4 , and Cyp2b9. We explored mRNA expression in 2 settings: (i) intact liver GH receptor (GHR) but altered GH and insulin-like growth factor 1 (IGF1) levels (NeuroDrd2KO, HiGH, aHepIGF1kd, and STAT5bCA mouse lines); and (ii) liver loss of GHR, with or without STAT5b reconstitution (aHepGHRkd, and aHepGHRkd + STAT5bCA). Lcn13 was downregulated in males in most models, while Asns and Cyp7b1 were decreased in males by low GH levels or action, or constant GH levels, but unexpectedly upregulated in both sexes by the loss of liver Igf1 or constitutive Stat5b expression. Hao , Cyp2a4 , and Cyp2b9 were generally decreased in female mice with low GH levels or action (NeuroDrd2KO and/or aHepGHRkd mice) and increased in HiGH females, while in contrast, Pgc1a was increased in female NeuroDrd2KO but decreased in STAT5bCA and aHepIGF1kd females. Bioinformatic analysis of RNAseq from aHepGHRkd livers stressed the greater impact of GHR loss on wide gene expression in males and highlighted that GH modifies almost completely different gene signatures in each sex. Concordantly, we show that altering different steps of the GH cascade in the liver modified liver expression of Lcn13 , Asns , Cyp7b1 , Hao2 , Hamp2 , Pgc1a , Cyp2a4 , and Cyp2b9 in a sex- and gene-specific manner. [ABSTRACT FROM AUTHOR]

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of secondary metabolites that have garnered scientific attention due to their complex scaffolds with potential roles in medicine, agriculture, and chemical ecology. RiPPs derive from the cleavage of ribosomally synthesized proteins and additional modifications, catalyzed by various enzymes to alter the peptide backbone or side chains. Of these enzymes, cytochromes P450 (P450s) are a superfamily of heme-thiolate proteins involved in many metabolic pathways, including RiPP biosyntheses. In this review, we focus our discussion on P450 involved in RiPP pathways and the unique chemical transformations they mediate. Previous studies have revealed a wealth of P450s distributed across all domains of life. While the number of characterized P450s involved in RiPP biosyntheses is relatively small, they catalyze various enzymatic reactions such as C–C or C–N bond formation. Formation of some RiPPs is catalyzed by more than one P450, enabling structural diversity. With the continuous improvement of the bioinformatic tools for RiPP prediction and advancement in synthetic biology techniques, it is expected that further cytochrome P450-mediated RiPP biosynthetic pathways will be discovered. Summary The presence of genes encoding P450s in gene clusters for ribosomally synthesized and post-translationally modified peptides expand structural and functional diversity of these secondary metabolites, and here, we review the current state of this knowledge. [ABSTRACT FROM AUTHOR]

Multiheme cytochromes play key roles in diverse biogeochemical cycles, but understanding the origin and evolution of these proteins is a challenge due to their ancient origin and complex structure. Up until now, the evolution of multiheme cytochromes composed by multiple redox modules in a single polypeptide chain was proposed to occur by gene fusion events. In this context, the pentaheme nitrite reductase NrfA and the tetraheme cytochrome c 554 were previously proposed to be at the origin of the extant octa- and nonaheme cytochrome c involved in metabolic pathways that contribute to the nitrogen, sulfur, and iron biogeochemical cycles by a gene fusion event. Here, we combine structural and character-based phylogenetic analysis with an unbiased root placement method to refine the evolutionary relationships between these multiheme cytochromes. The evidence show that NrfA and cytochrome c 554 belong to different clades, which suggests that these two multiheme cytochromes are products of truncation of ancestral octaheme cytochromes related to extant octaheme nitrite reductase and MccA, respectively. From our phylogenetic analysis, the last common ancestor is predicted to be an octaheme cytochrome with nitrite reduction ability. Evolution from this octaheme framework led to the great diversity of extant multiheme cytochromes analyzed here by pruning and grafting of protein modules and hemes. By shedding light into the evolution of multiheme cytochromes that intervene in different biogeochemical cycles, this work contributes to our understanding about the interplay between biology and geochemistry across large time scales in the history of Earth. [ABSTRACT FROM AUTHOR]

We use first principles of population genetics to model the evolution of proteins under persistent positive selection (PPS). PPS may occur when organisms are subjected to persistent environmental change, during adaptive radiations, or in host–pathogen interactions. Our mutation–selection model indicates protein evolution under PPS is an irreversible Markov process, and thus proteins under PPS show a strongly asymmetrical distribution of selection coefficients among amino acid substitutions. Our model shows the criteria ω > 1 (where ω is the ratio of nonsynonymous over synonymous codon substitution rates) to detect positive selection is conservative and indeed arbitrary, because in real proteins many mutations are highly deleterious and are removed by selection even at positively selected sites. We use a penalized-likelihood implementation of the PPS model to successfully detect PPS in plant RuBisCO and influenza HA proteins. By directly estimating selection coefficients at protein sites, our inference procedure bypasses the need for using ω as a surrogate measure of selection and improves our ability to detect molecular adaptation in proteins. [ABSTRACT FROM AUTHOR]

Major depressive disorder (MDD) is a common psychiatric illness that manifests in sex-influenced ways. Men and women may experience depression differently and also respond to various antidepressant treatments in sex-influenced ways. Ketamine, which is now being used as a rapid-acting antidepressant, is likely the same. To date, the majority of studies investigating treatment outcomes in MDD do not disaggregate the findings in males and females, and this is also true for ketamine. This review aims to highlight that gap by exploring pre-clinical data—at a behavioral, molecular, and structural level—and recent clinical trials. Sex hormones, particularly estrogen and progesterone, influence the response at all levels examined, and sex is therefore a critical factor to examine when looking at ketamine response. Taken together, the data show females are more sensitive to ketamine than males, and it might be possible to monitor the phase of the menstrual cycle to mitigate some risks associated with the use of ketamine for females with MDD. Based on the studies reviewed in this article, we suggest that ketamine should be administered adhering to sex-specific considerations. [ABSTRACT FROM AUTHOR]

During photosynthesis, electrons are transferred between the cytochrome b 6 f complex and photosystem I. This is carried out by the protein plastocyanin in plant chloroplasts, or by either plastocyanin or cytochrome c 6 in many cyanobacteria and eukaryotic algal species. There are three further cytochrome c 6 homologs: cytochrome c 6A in plants and green algae, and cytochromes c 6B and c 6C in cyanobacteria. The function of these proteins is unknown. Here, we present a comprehensive analysis of the evolutionary relationship between the members of the cytochrome c 6 family in photosynthetic organisms. Our phylogenetic analyses show that cytochromes c 6B and c 6C are likely to be orthologs that arose from a duplication of cytochrome c 6, but that there is no evidence for separate origins for cytochromes c 6B and c 6C. We therefore propose renaming cytochrome c 6C as cytochrome c 6B. We show that cytochrome c 6A is likely to have arisen from cytochrome c 6B rather than by an independent duplication of cytochrome c 6, and present evidence for an independent origin of a protein with some of the features of cytochrome c 6A in peridinin dinoflagellates. We conclude with a new comprehensive model of the evolution of the cytochrome c 6 family which is an integral part of understanding the function of the enigmatic cytochrome c 6 homologs. [ABSTRACT FROM AUTHOR]

In recent years, efforts to exploit sunlight, a free and abundant energy source, have sped up dramatically. Oxygenic photosynthetic organisms, such as higher plants, algae, and cyanobacteria, can convert solar energy into chemical energy very efficiently using water as an electron donor. By providing organic building blocks for life in this way, photosynthesis is undoubtedly one of the most important processes on Earth. The aim of light-driven catalysis is to harness solar energy, in the form of reducing power, to drive enzymatic reactions requiring electrons for their catalytic cycle. Light-driven enzymes have been shown to have a large number of biotechnological applications, ranging from the production of high-value secondary metabolites to the development of green chemistry processes. Here, we highlight recent key developments in the field of light-driven catalysis using biological components. We will also discuss strategies to design and optimize light-driven systems in order to develop the next generation of sustainable solutions in biotechnology. [ABSTRACT FROM AUTHOR]

Cannabis has been used as a medicinal plant for thousands of years. As a result of centuries of breeding and selection, there are now over 700 varieties of cannabis that contain hundreds of compounds, including cannabinoids and terpenes. Cannabinoids are fatty compounds that are the main biological active constituents of cannabis. Terpenes are volatile compounds that occur in many plants and have distinct odors. Cannabinoids exert their effect on the body by binding to receptors, specifically cannabinoid receptors types 1 and 2. These receptors, together with endogenous cannabinoids and the systems for synthesis, transport, and degradation, are called the Endocannabinoid System. The two most prevalent and commonly known cannabinoids in the cannabis plant are delta-9-tetrahydrocannabinol (THC) and cannabidiol. The speed, strength, and type of effects of cannabis vary based on the route of administration. THC is rapidly distributed through the body to fatty tissues like the brain and is metabolized by the cytochrome P450 system to 11-hydroxy-THC, which is also psychoactive. Cannabis and cannabinoids have been indicated for several medical conditions. There is evidence of efficacy in the symptomatic treatment of nausea and vomiting, pain, insomnia, post-traumatic stress disorder, anxiety, loss of appetite, Tourette’s syndrome, and epilepsy. Cannabis has also been associated with treatment for glaucoma, Huntington’s Disease, Parkinson’s Disease, and dystonia, but there is not good evidence to support its efficacy. Side effects of cannabis include psychosis and anxiety, which can be severe. Here, we provided a summary of the history of cannabis, its pharmacology, and its medical uses. [ABSTRACT FROM AUTHOR]

Cytochrome P450 monooxygenases (P450s) play important roles in metabolizing various insecticides and often contribute to the development of insecticide resistance in insects and other arthropod species. The objective of this study was to compare the metabolism of four commonly used pyrethroids including deltamethrin, fluvalinate, fenvalerate, and permethrin in the midgut tissue of Locusta migratoria Linnaeus (Orthoptera: Acrididae) by using synergism bioassay and ultra-performance liquid chromatography (UPLC)–mass spectrometer (MS) analyses. Our study showed that piperonyl butoxide (PBO, P450 enzyme inhibitor) can significantly synergize the toxicity of deltamethrin, fluvalinate, and fenvalerate with synergism ratios ranging from 1.30 to 1.70 folds. Preincubations of the midgut tissue with PBO followed by incubations with each of the four pyrethroids resulted in significantly higher amounts of unmetabolized deltamethrin and fluvalinate than those in the control (preincubation without PBO) as well as preincubations with other two detoxification enzyme inhibitors. These results indicate that P450s play important roles in metabolizing deltamethrin and fluvalinate in the midgut tissue. Our further study using deltamethrin as a representative pyrethroid and UPLC–MS techniques confirmed that the reduced amount of deltamethrin in the control (preincubation without PBO) was due to the metabolism of deltamethrin to yield hydroxydeltamethrin which is a major metabolite produced by P450-mediated aromatic hydroxylation of deltamethrim. These results provide new insights into differential metabolic activity of P450s towards different pyrethroids in the midgut tissue of L. migratoria. [ABSTRACT FROM AUTHOR]

Two cytochromes c5 (SBcytc and SVcytc) have been derived from Shewanella living in the deep-sea, which is a high pressure environment, so it could be that these proteins are more stable at high pressure than at atmospheric pressure, 0.1 MPa. This study, however, revealed that SBcytc and SVcytc were more stable at 0.1 MPa than at higher pressure. In addition, at 0.1-150 MPa, the stability of SBcytc and SVcytc was higher than that of homologues from atmospheric-pressure Shewanella, which was due to hydrogen bond formation with the heme in the former two proteins. This study further revealed that cytochrome c551 (PMcytc) of deep-sea Pseudomonas was more stable than a homologue of atmospheric-pressure Pseudomonas aeruginosa, and that specific hydrogen bond formation with the heme also occurred in the former. Although SBcytc and SVcytc, and PMcytc are phylogenetically very distant, these deep-sea cytochromes c are commonly stabilized through hydrogen bond formation. [ABSTRACT FROM AUTHOR]

Long-term cultures of primary adult rat hepatocytes were used to study the effects of N-acetyl-2-aminofluorene (AAF) on hepatocyte proliferation during the growth cycle; on the initiation of hepatocyte DNA synthesis in quiescent cultures; an-- on hepatocyte DNA replication following the initiation of DNA synthesis. Scatchard analyses were used to identify the pharmacologic properties of radiolabeled AAF metabolite binding to hepatocyte macromolecules. Two classes of growth cycle-dependent AAF metabolite binding sites--a high-affinity low-capacity site (designated Site I) and a low-affinity highcapacity site (designated Site II)--associated with two spatially distinct classes of macromolecular targets, were revealed. Based upon radiolabeled AAF metabolite binding to purified hepatocyte genomic DNA or to DNA, RNA, proteins and lipids from isolated nuclei, Site IDAY 4 targets (KD[APPARENT]≈2-4x10-6M and BMAX[APPARENT]≈6 pmol/106 cells/24 h) were consistent with genomic DNA; and with AAF metabolized by a nuclear cytochrome P450. Based upon radiolabeled AAF binding to total cellular lysates, Site IIDAY 4 targets (KD[APPARENT]≈1.5x10-3M and BMAX[APPARENT]≈350 pmol/106 cells/24 h) were consistent with cytoplasmic proteins; and with AAF metabolized by cytoplasmic cytochrome P450s. DNA synthesis was not inhibited by concentrations of AAF that saturated DNA binding in the neighborhood of the Site I KD. Instead, hepatocyte DNA synthesis inhibition required higher concentrations of AAF approaching the Site II KD. These observations raise the possibility that carcinogenic DNA adducts derived from AAF metabolites form below concentrations of AAF that inhibit replicative and repair DNA synthesis. [ABSTRACT FROM AUTHOR]

Next-generation sequencing methods enable identification of the genetic basis of traits in species that have no prior genomic information available. The combination of next-generation sequencing, variant analysis, and linkage is a powerful way of identifying candidate genes for a trait of interest. Here, we used a comparative transcriptomics [RNA sequencing (RNAseq)] and genetic linkage analysis approach to identify the rph1 gene. rph1 variants are responsible for resistance to the fumigant phosphine (PH3) that is used to control insect pests of stored grain. In each of the four major species of pest insect of grain we have investigated, there are two major resistance genes, rph1 and rph2, which interact synergistically to produce strongly phosphine-resistant insects. Using RNAseq and genetic linkage analyses, we identified candidate resistance (rph1) genes in phosphine-resistant strains of three species: Rhyzopertha dominica (129 candidates), Sitophilus oryzae (206 candidates), and Cryptolestes ferrugineus (645 candidates). We then compared these candidate genes to 17 candidate resistance genes previously mapped in Tribolium castaneum and found only one orthologous gene, a cytochrome b5 fatty acid desaturase (Cyt-b5-r), to be associated with the rph1 locus in all four species. This gene had either missense amino acid substitutions and/or insertion/deletions/frameshift variants in each of 18 phosphine-resistant strains that were not observed in the susceptible strains of the four species. We propose a model of phosphine action and resistance in which phosphine induces lipid peroxidation through reactive oxygen species generated by dihydrolipoamide dehydrogenase, whereas disruption of Cyt-b5-r in resistant insects decreases the polyunsaturated fatty acid content of membranes, thereby limiting the potential for lipid peroxidation. [ABSTRACT FROM AUTHOR]

Background: The AsperGenius® assay is a multiplex real-time PCR test that allows the simultaneous detection of Aspergillus species and identification of the most common mutations in the Aspergillus fumigatus cyp51A gene conferring resistance (TR34/L98H and TR46/T289A/Y121F) by using melting curve analysis. Mixed infections with azole-resistant and susceptible A. fumigatus have rarely been described.Methods: The AsperGenius® multiplex real-time PCR assay (PathoNostics, Maastricht, the Netherlands) was used on bronchoalveolar lavage (BAL) samples of 91 consecutive patients with a suspected invasive Aspergillus infection at the Erasmus MC University Medical Center, Rotterdam.Results: In three cases the AsperGenius® assay indicated the simultaneous presence of WT and mutant genes (two patients with TR34/L98H mutation and one patient with TR46/T289A/Y121F mutation) and therefore mixed infections with azole-susceptible and -resistant isolates. In one of the three cases, the mixed infection was confirmed by phenotypic antifungal testing of multiple A. fumigatus colonies.Conclusions: The use of a dedicated A. fumigatus cyp51A resistance PCR allowed the detection of mixed infections with azole-resistant and -susceptible Aspergillus strains. These mixed infections may remain undiagnosed with conventional phenotypic susceptibility testing. [ABSTRACT FROM AUTHOR]

Autosomal recessive congenital ichthyosis ( ARCI) caused by mutations in CYP4F22 is very rare. CyP4F22, a protein of the cytochrome-P450 family 4, encodes an epidermal ω-hydroxylase decisive in the formation of acylceramides, which is hypothesized to be crucial for skin-barrier function. We report a girl with consanguineous parents presenting as collodion baby with contractures of the great joints and palmoplantar hyperlinearity. In the course of the disease she developed fine scaling of the skin with erythroderma, the latter disappearing until the age of 6 months. Her sister showed a generalized fine-scaling phenotype, and, interestingly, was born without a collodion membrane. The analysis of all known candidate genes for ARCI in parallel with a next-generation sequencing approach using a newly designed dermatogenetics gene panel revealed a previously unknown homozygous splice-site mutation c.549+5G>C in CYP4F22 in both girls, confirming the diagnosis of ARCI. Ultrastructural analysis by transmission electron microscopy in both patients showed epidermal hyperplasia, orthohyperkeratosis with persistence of corneodesmosomes into the outer stratum corneum layers, fragmented and disorganized lamellar lipid bilayers, which could be ascribed to inhomogeneous lamellar body secretion, as well as lamellar body and lipid entombment in the corneocytes. These findings correlated with increased transepidermal water loss on the functional level. For the first time, we report a collodion baby phenotype and epidermal barrier impairment in CyP4F22-deficient epidermis at both the ultrastructural and functional level, and corroborate the importance of CyP4F22 for epidermal maturation and barrier function. [ABSTRACT FROM AUTHOR]

Objectives Non-alcoholic fatty liver disease ( NAFLD) is associated with impaired liver function, and resveratrol could suppress NAFLD progression. This study examined the effects of NAFLD on the expression of major cytochrome P450 ( CYP) subtypes in the liver and whether the expression could be attenuated by resveratrol. Methods C57 BL/6 mice (male, 10 weeks of age) were fed a high-fat and high-sucrose ( HFHS) diet to induce NAFLD. Major Cyp subtype mRNA expression in the liver was measured by real-time RT- PCR. Key findings Body and liver weights at 4 and 12 weeks were significantly higher in mice fed the HFHS diet compared with control. The HFHS diet significantly increased the accumulation of cholesterol and triglycerides at 12 weeks. Under this condition, the HFHS diet increased the expression of Cyp1a2 and decreased that of Cyp3a11 at 1 week and thereafter. On the other hand, Cyp1a1, 2b10 and 2c29 mRNA expression levels in the liver were significantly increased at 12 weeks only. Resveratrol (0.05% (w/w) in diet) slightly suppressed lipid accumulation in the liver, but failed to recover impaired Cyp gene expression levels in NAFLD. Conclusions Drug metabolism may be impaired in NAFLD, and each Cyp subtype is regulated in a different manner. [ABSTRACT FROM AUTHOR]

We here reported the mitochondrial (mt) genome of one of the heterotrophic microeukaryotes related to cryptophytes, Palpitomonas bilix. The P. bilix mt genome was found to be a linear molecule composed of "single copy region" (~16 kb) and repeat regions (~30 kb) arranged in an inverse manner at both ends of the genome. Linear mt genomes with large inverted repeats are known for three distantly related eukaryotes (including P. bilix), suggesting that this particular mt genome structure has emerged at least three times in the eukaryotic tree of life. The P. bilixmt genome contains 47 protein-coding genes including ccmA, ccmB, ccmC, and ccmF, which encode protein subunits involved in the system for cytochrome c maturation inherited from a bacterium (System I). We present data indicating that the phylogenetic relatives of P. bilix, namely, cryptophytes, goniomonads, and kathablepharids, utilize an alternative system for cytochrome c maturation, which has most likely emerged during the evolution of eukaryotes (System III). To explain the distribution of Systems I and III in P. bilix and its phylogenetic relatives, two scenarios are possible: (i) System I was replaced by System III on the branch leading to the common ancestor of cryptophytes, goniomonads, and kathablepharids, and (ii) the two systems co-existed in their common ancestor, and lost differentially among the four descendants. [ABSTRACT FROM AUTHOR]

The article comments on Ticagrelor or Clopidogrel with Aspirin in High-Risk Patients with Acute Nondisabling Cerebrovascular Events II (CHANCE-2) clinical trial involving patients with a minor ischaemic stroke or transient ischaemic attack. Topics include CHANCE-2's objective to test the efficacy of dual antiplatelet therapy with ticagrelor and aspirin over clopidogrel and aspirin in reducing the risk of subsequent stroke in CYP2C19 loss-of-function carrier, and the limitations of CHANCE-2.

A sodium pentobarbital-induced sleep time (ST) study was conducted on intact males, Boer x Spanish goats (n = 30), selected for high (J+) or low juniper (J-) consumption with the objective to compare the Phase I detoxification system of the genetic divergent lines (EBV of 13.1 ± 0.2 and -14.2 ± 0.3, respectively). The ST study was conducted following a minimum period of 21 days on three different diets: grazing juniper infested rangeland (JIR), forage diet with no monoterpenes (M0), and forage diet with 8 g/kg added camphor, sabinene, and a-pinene monoterpenes in a ratio of 5:4:1 (M+). Fecal samples from goats on the JIR and M+ diets were analyzed for camphor and sabinene, and, when on the JIR diet, analyzed for percentage juniper in the diet using previously developed NIRS calibrations. Data were submitted to ANOVA analysis with repeated measures, assuming as significant when alpha was less than 10% (P < 0.10) by the F test. Percentage of juniper in the diet of J+ goats on JIP (38.6 ± 3.4%) was greater (P < 0.001) than J-goats (28.0 ± 3.8%). The J+ goats slept 15.1 (P = 0.02), 14.3 (P = 0.06), and 15.8 (P = 0.06) minutes longer than Jgoats on JIR, M0, and M+ diets, respectively. There was no difference in ST between diets, and there was no interaction line × diet. Goats from the J+ line had higher concentrations of camphor in their feces on the JIR (P = 0.07) and M+ (P = 0.09) diets, while sabinene concentration was similar. Goats selected for juniper consumption had longer ST than J-goats which indicates a less efficient Phase I detoxification system, probably because there were less monoterpenes in the blood to be metabolized in the liver by the cytochromes P450 enzymes. [ABSTRACT FROM AUTHOR]

Communication signals are highly diverse traits. This diversity is usually assumed to be shaped by selective forces, whereas the null hypothesis of divergence through drift is often not considered. In Panama, the weakly electric fish Brachyhypopomus occidentalis is widely distributed in multiple independent drainage systems, which provide a natural evolutionary laboratory for the study of genetic and signal divergence in separate populations. We quantified geographic variation in the electric signals of 109 fish from five populations, and compared it to the neutral genetic variation estimated from cytochrome oxidase I (COI) sequences of the same individuals, to test whether drift may be driving divergence of their signals. Signal distances were highly correlated with genetic distances, even after controlling for geographic distances, suggesting that drift alone is sufficient to explain geographic variation in electric signals. Significant differences at smaller geographic scales (within drainages) showed, however, that electric signals may evolve at a faster rate than expected under drift, raising the possibility that additional adaptive forces may be contributing to their evolution. Overall, our data point to stochastic forces as main drivers of signal evolution in this species and extend the role of drift in the evolution of communication systems to fish and electrocommunication. [ABSTRACT FROM AUTHOR]

Populations of the Malagasy H ipposideros commersoni (family Hipposideridae) are threatened by deforestation and hunting. Maximum likelihood and Bayesian analysis of 148 cytochrome b sequences found this species to be paraphyletic and composed of three well-supported monophyletic clades. Clades B and C form a monophyletic lineage that can be referred to H. commersoni; these two clades are separated by 6% sequence variation. Clade A represents a distinct evolutionary lineage separate (9-11% average sequence divergence) from H. commersoni (clades B and C) and is named herein as a new species, H ipposideros cryptovalorona sp. nov. In the phylogeny presented herein, this species is strongly associated with the outgroup taxa H ipposideros gigas and H ipposideros vittatus, both restricted to Africa. External, cranial and dental measurements taken from the same individuals used in the molecular study indicate no clear distinction in morphology amongst these three clades; this includes noseleaf structure and craniodental characteristics. Principal component analyses showed limited separation of the three clades. Comparison to a Quaternary fossil species from north-west Madagascar, H ipposideros besaoka, found little morphological overlap between any of the three clades and this extinct species. Hence, at least three species of H ipposideros have occurred on Madagascar since the Late Pleistocene, two extant ( H. commersoni s.s. and H. cryptovalorona sp. nov.) and one extinct ( H. besaoka). © 2015 The Linnean Society of London [ABSTRACT FROM AUTHOR]

Photosynthetic organisms have the ability to adapt to changes in light quality by readjusting the cross sections of the light-harvesting systems of photosystem II (PSII) and photosystem I (PSI). This process, called state transitions, maintains the redox poise of the photosynthetic electron transfer chain and ensures a high photosynthetic yield when light is limiting. It is mediated by the Stt7/STN7 protein kinase, which is activated through the cytochrome b6f complex upon reduction of the plastoquinone pool. Its probable major substrate, the light-harvesting complex of PSII, once phosphorylated, dissociates from PSII and docks to PSI, thereby restoring the balance of absorbed light excitation energy between the two photosystems. Although the kinase is known to be inactivated under high-light intensities, the molecular mechanisms governing its regulation remain unknown. In this study we monitored the redox state of a conserved and essential Cys pair of the Stt7/STN7 kinase and show that it forms a disulfide bridge. We could not detect any change in the redox state of these Cys during state transitions and high-light treatment. It is only after prolonged anaerobiosis that this disulfide bridge is reduced. It is likely to be mainly intramolecular, although kinase activation may involve a transient covalently linked kinase dimer with two intermolecular disulfide bonds. Using the yeast two-hybrid system, we have mapped one interaction site of the kinase on the Rieske protein of the cytochrome b6f complex. [ABSTRACT FROM AUTHOR]

Background. Vitiligo is associated with various autoimmune disorders, and organspecific autoantibodies are frequently found in patients with this disorder. Vitiligo is classically divided into segmental vitiligo (SV) and nonsegmental vitiligo (NSV), and it is believed that the pathogenesis differs between these two types. As the NSV type is related to an autoimmune mechanism, autoantibody detection rates are likely to be higher in the NSV type than in the segmental type; however, no comparative studies have been performed. Aim. To analyse the rates of autoantibody positivity according to the clinical features in patients with vitiligo. Methods. Rates of antithyroid antibody (Tg Ab), antinuclear antibody (ANA) and thyroid peroxidase antibody (TPO Ab) positivity were analysed and compared according to the sex, clinical type and age of onset of 807 patients with vitiligo. Results. There were 106 patients with SV (13.1%) and 701 patients with NSV (86.9%). Tg Ab and ANA positivity did not differ between the SV and NSV types. A positive TPO Ab result was obtained in 16 patients with SV (15.1%) and 173 patients with NSV (24.7%). The TPO Ab positivity rate was significantly higher in NSV (X2 = 4.14, P < 0.05). The positivity rates of the three autoantibodies differed significantly according to age of onset (P = 0.001, P = 0.02 and P < 0.001 for Tg Ab, ANA and TPO Ab positivity, respectively). The TPO Ab positivity rate also showed a sex difference (P < 0.001). Conclusions. The positivity rates for the three autoantibodies showed differences according to age of onset and sex. The rates of Tg Ab and ANA positivity showed no significant differences according to clinical type, but the TPO Ab positivity rate was significantly different between SV and NSV. It appears likely that an autoimmune mechanism contributes to the pathogenesis of SV. [ABSTRACT FROM AUTHOR]

Polychlorinated biphenyls (PCBs) are durable and widely distributed environmental contaminants that can compromise the normal functions of multiple organs and systems; one important mechanism is the induction of inflammatory disorders. In this study, we explored the influences of 2,3',4,4',5-pentachlorobiphenyl (PCB118) on inflammatory responses and its underlying mechanisms in the thyroid. Wistar rats were administered PCB118 intraperitoneally at 0, 10, 100, and 1000 αμg/kg/ d, 5 days a week for 13 weeks; rat thyroid FRTL-5 cells were treated with PCB118 (0, 0.25, 2.5, and 25 nM) for indicated time. Results revealed that PCB118 promoted the generation of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and intercellular adhesion molecule-1 (ICAM-1) in a time- and dose-related manner and decreased sodium/iodide symporter (NIS) protein expression. Moreover, stimulation with PCB118 resulted in the upregulation of the aryl hydrocarbon receptor (AhR)-responsive gene cytochrome P450 1A1 in FRTL-5 cells; whereas pretreatment with the AhR inhibitor anaphthoflavone or AhR small interfering RNA (siRNA) suppressed AhR, CYP1A1, IL-6, and ICAM-1 and restored NIS expression. In vivo and in vitro studies also suggested that the c-Jun N-terminal kinase (JNK) pathway was activated on PCB118 exposure, and the experiments using siRNA for JNK partially blocked PCB118-induced upregulation of IL-6 and ICAM-1 and downregulation of NIS. Altogether, PCB118 stimulates production of IL-6, TNF-α, and ICAM-1 in the thyroid through AhR and JNK activations and subsequently interferes with NIS expression, resulting in the disruption of thyroid structure and function. [ABSTRACT FROM AUTHOR]

Motivation: Cytochrome P450 (CYP) is a superfamily of enzymes responsible for the metabolism of drugs, xenobiotics and endogenous compounds. CYP2D6 metabolizes about 30% of drugs and predicting potential CYP2D6 inhibition is important in early-stage drug discovery. Results: We developed an original in silico approach for the prediction of CYP2D6 inhibition combining the knowledge of the protein structure and its dynamic behavior in response to the binding of various ligands and machine learning modeling. This approach includes structural information for CYP2D6 based on the available crystal structures and molecular dynamic simulations (MD) that we performed to take into account conformational changes of the binding site. We performed modeling using three learning algorithms -support vector machine, RandomForest and NaiveBayesian -and we constructed combined models based on topological information of known CYP2D6 inhibitors and predicted binding energies computed by docking on both X-ray and MD protein conformations. In addition, we identified three MD-derived structures that are capable all together to better discriminate inhibitors and non-inhibitors compared with individual CYP2D6 conformations, thus ensuring complementary ligand profiles. Inhibition models based on classical molecular descriptors and predicted binding energies were able to predict CYP2D6 inhibition with an accuracy of 78% on the training set and 75% on the external validation set. [ABSTRACT FROM AUTHOR]

Chlamydomonas sp. UWO 241 (UWO 241) is a psychrophilic green alga isolated from Antarctica. A unique characteristic of this algal strain is its inability to undergo state transitions coupled with the absence of photosystem II (PSII) light-harvesting complex protein phosphorylation. We show that UWO 241 preferentially phosphorylates specific polypeptides associated with an approximately 1,000-kD pigment-protein supercomplex that contains components of both photosystem I (PSI) and the cytochrome b6/f (Cyt b6/f) complex. Liquid chromatography nano-tandem mass spectrometry was used to identify three major phosphorylated proteins associated with this PSI-Cyt b6/f supercomplex, two 17-kD PSII subunit P-like proteins and a 70-kD ATP-dependent zinc metalloprotease, FtsH. The PSII subunit P-like protein sequence exhibited 70.6% similarity to the authentic PSII subunit P protein associated with the oxygen-evolving complex of PSII in Chlamydomonas reinhardtii. Tyrosine-146 was identified as a unique phosphorylation site on the UWO 241 PSII subunit P-like polypeptide. Assessment of PSI cyclic electron transport by in vivo P700 photooxidation and the dark relaxation kinetics of P700+ indicated that UWO 241 exhibited PSI cyclic electron transport rates that were 3 times faster and more sensitive to antimycin A than the mesophile control, Chlamydomonas raudensis SAG 49.72. The stability of the PSI-Cyt b6/f supercomplex was dependent upon the phosphorylation status of the PsbP-like protein and the zinc metalloprotease FtsH as well as the presence of high salt. We suggest that adaptation of UWO 241 to its unique low-temperature and high-salt environment favors the phosphorylation of a PSI-Cyt b6/f supercomplex to regulate PSI cyclic electron transport rather than the regulation of state transitions through the phosphorylation of PSII light-harvesting complex proteins. [ABSTRACT FROM AUTHOR]

Three primary factors affecting genetic patterns of marine species in the Northwestern Pacific Ocean have been proposed: isolation and population expansion during Pleistocene glacial cycles, ocean currents facilitating the gene flow, and the Yangtze River outflow imposing a physical barrier to gene flow. Here, we examined these factors affecting population structuring of the Asian paddle crab, Charybdis japonica, in the Yellow Sea, East China Sea, and adjacent areas. Genetic variation in nine populations of C. japonica (n = 169) was determined from partial mitochondrial cytochrome c oxidase subunit I sequences. Among the 14 haplotypes identified, a dominant haplotype H1 was present in all populations, and a relatively abundant localized haplotype H2 was found in four of the northern populations. Furthermore, the frequency of the common haplotype H1 decreased from south to north. A genetic discontinuity was detected in Haizhou Bay, which divided species into two groups (north group and south group). The lack of genetic structure in the south and north groups indicates high dispersal of C. japonica within groups. Local marine gyres in Haizhou Bay might be responsible for the divergence of the north and south groups. Our study highlights the importance of local marine gyres for influencing genetic structure in marine coastal species in the Northwestern Pacific, especially in species spawning inshore. [ABSTRACT FROM AUTHOR]

During desiccation, homoiochlorophyllous resurrection plants retain most of their photosynthetic apparatus, allowing them to resume photosynthetic activity quickly upon water availability. These plants rely on various mechanisms to prevent the formation of reactive oxygen species and/or protect their tissues from the damage they inflict. In this work, we addressed the issue of how homoiochlorophyllous resurrection plants deal with the problem of excessive excitation/electron pressures during dehydration using Craterostigma pumilum as a model plant. To investigate the alterations in the supramolecular organization of photosynthetic protein complexes, we examined cryoimmobilized, freeze-fractured leaf tissues using (cryo)scanning electron microscopy. These examinations revealed rearrangements of photosystem II (PSII) complexes, including a lowered density during moderate dehydration, consistent with a lower level of PSII proteins, as shown by biochemical analyses. The latter also showed a considerable decrease in the level of cytochrome f early during dehydration, suggesting that initial regulation of the inhibition of electron transport is achieved via the cytochrome b6f complex. Upon further dehydration, PSII complexes are observed to arrange into rows and semicrystalline arrays, which correlates with the significant accumulation of sucrose and the appearance of inverted hexagonal lipid phases within the membranes. As opposed to PSII and cytochrome f, the light-harvesting antenna complexes of PSII remain stable throughout the course of dehydration. Altogether, these results, along with photosynthetic activity measurements, suggest that the protection of retained photosynthetic components is achieved, at least in part, via the structural rearrangements of PSII and (likely) light-harvesting antenna complexes into a photochemically quenched state. [ABSTRACT FROM AUTHOR]

Diverse signaling pathways are activated by perturbation of mitochondrial function under different growth conditions. Mitochondria have emerged as an important organelle for sensing and coping with stress in addition to being the sites of important metabolic pathways. Here, responses to moderate light and drought stress were examined in different Arabidopsis (Arabidopsis thaliana) mutant plants lacking a functional alternative oxidase (alternative oxidase1a [aox1a]), those with reduced cytochrome electron transport chain capacity (T3/T7 bacteriophage-type RNA polymerase, mitochondrial, and plastidial [rpoTmp]), and double mutants impaired in both pathways (aox1a:rpoTmp). Under conditions considered optimal for growth, transcriptomes of aox1a and rpoTmp were distinct. Under adverse growth conditions, however, transcriptome changes in aox1a and rpoTmp displayed a highly significant overlap and were indicative of a common mitochondrial stress response and downregulation of photosynthesis. This suggests that the role of mitochondria to support photosynthesis is provided through either the alternative pathway or the cytochrome pathway, and when either pathway is inhibited, such as under environmental stress, a common, dramatic, and succinct mitochondrial signal is activated to alter energy metabolism in both organelles. aox1a:rpoTmp double mutants grown under optimal conditions showed dramatic reductions in biomass production compared with aox1a and rpoTmp and a transcriptome that was distinct from aox1a or rpoTmp. Transcript data indicating activation of mitochondrial biogenesis in aox1a:rpoTmp were supported by a proteomic analysis of over 200 proteins. Under optimal conditions, aox1a: rpoTmp plants seemed to switch on many of the typical mitochondrial stress regulators. Under adverse conditions, aox1a:rpoTmp turned off these responses and displayed a biotic stress response. Taken together, these results highlight the diverse signaling pathways activated by the perturbation of mitochondrial function under different growth conditions. [ABSTRACT FROM AUTHOR]

Diverse signaling pathways are activated by perturbation of mitochondrial function under different growth conditions. Mitochondria have emerged as an important organelle for sensing and coping with stress in addition to being the sites of important metabolic pathways. Here, responses to moderate light and drought stress were examined in different Arabidopsis (Arabidopsis thaliana) mutant plants lacking a functional alternative oxidase (alternative oxidase1a [aox1a]), those with reduced cytochrome electron transport chain capacity (T3/T7 bacteriophage-type RNA polymerase, mitochondrial, and plastidial [rpoTmp]), and double mutants impaired in both pathways (aox1a:rpoTmp). Under conditions considered optimal for growth, transcriptomes of aox1a and rpoTmp were distinct. Under adverse growth conditions, however, transcriptome changes in aox1a and rpoTmp displayed a highly significant overlap and were indicative of a common mitochondrial stress response and downregulation of photosynthesis. This suggests that the role of mitochondria to support photosynthesis is provided through either the alternative pathway or the cytochrome pathway, and when either pathway is inhibited, such as under environmental stress, a common, dramatic, and succinct mitochondrial signal is activated to alter energy metabolism in both organelles. aox1a:rpoTmp double mutants grown under optimal conditions showed dramatic reductions in biomass production compared with aox1a and rpoTmp and a transcriptome that was distinct from aox1a or rpoTmp. Transcript data indicating activation of mitochondrial biogenesis in aox1a:rpoTmp were supported by a proteomic analysis of over 200 proteins. Under optimal conditions, aox1a: rpoTmp plants seemed to switch on many of the typical mitochondrial stress regulators. Under adverse conditions, aox1a:rpoTmp turned off these responses and displayed a biotic stress response. Taken together, these results highlight the diverse signaling pathways activated by the perturbation of mitochondrial function under different growth conditions. [ABSTRACT FROM AUTHOR]

The article reports on the effects of ritonavir and cobicistat on dolutegravir exposure which is used in the treatment of HIV infection. Topics include a survey on HIV-infected patients switching from darunavir and ritonavir drug to darunavir and cobicistat; use of therapeutic drug monitoring for the same; and the analysis of difference between ritonavir and cobicistat in terms of selectivity for cytochrome inhibition, patterns of modulation of phase II metabolic enzymes, and drug transporters.

Magnetotactic bacteria use a specific set of conserved proteins to biomineralize crystals of magnetite or greigite within their cells in organelles called magnetosomes. Using Magnetospirillum magneticum AMB-1, we examined one of the magnetotactic bacteria-specific conserved proteins named Mam P that was recently reported as a new type of cytochrome c that has iron oxidase activity. We found that Mam P is a membrane-bound cytochrome, and the MamP content increases during the exponential growth phase compared to two other magnetosome-associated proteins on the same operon, Mam A and Mam K. To assess the function of Mam P, we overproduced Mam P from plasmids in wild-type ( WT) AMB-1 and found that during the exponential phase of growth, these cells contained more magnetite crystals that were the same size as crystals in WT cells. Conversely, when the heme c-binding motifs within the mamP on the plasmid was mutated, the cells produced the same number of crystals, but smaller crystals than in WT cells during exponential growth. These results strongly suggest that during the exponential phase of growth, Mam P is crucial to the normal growth of magnetite crystals during biomineralization. [ABSTRACT FROM AUTHOR]

Quinol oxidation in the catalytic quinol oxidation site (Qo site) of cytochrome (cyt) bc1 complexes is the key step of the Q cycle mechanism, which laid the ground for Mitchell’s chemiosmotic theory of energy conversion. Bifurcated electron transfer upon quinol oxidation enables proton uptake and release on opposite membrane sides, thus generating a proton gradient that fuels ATP synthesis in cellular respiration and photosynthesis. The Qo site architecture formed by cyt b and Rieske iron–sulfur protein (ISP) impedes harmful bypass reactions. Catalytic importance is assigned to four residues of cyt b formerly described as PEWY motif in the context of mitochondrial complexes, which we now denominate Qo motif as comprehensive evolutionary sequence analysis of cyt b shows substantial natural variance of the motif with phylogenetically specific patterns. In particular, the Qo motif is identified as PEWY in mitochondria, α- and ε-Proteobacteria, Aquificae, Chlorobi, Cyanobacteria, and chloroplasts. PDWY is present in Gram-positive bacteria, Deinococcus–Thermus and haloarchaea, and PVWY in β- and γ-Proteobacteria. PPWF only exists in Archaea. Distinct patterns for acidophilic organisms indicate environment-specific adaptations. Importantly, the presence of PDWY and PEWY is correlated with the redox potential of Rieske ISP and quinone species. We propose that during evolution from low to high potential electron-transfer systems in the emerging oxygenic atmosphere, cyt bc1 complexes with PEWY as Qo motif prevailed to efficiently use high potential ubiquinone as substrate, whereas cyt b with PDWY operate best with low potential Rieske ISP and menaquinone, with the latter being the likely composition of the ancestral cyt bc1 complex. [ABSTRACT FROM PUBLISHER]

The article presents a study focusing on the decrease of hepatic cytochrome P-450 in scurvy-prone osteogenic disorder Shionogi (ODS) rats by the deficiency of ascorbic acid. The findings include the decrease of hepatic cytochrome P-450, especially CYP2B1/2B in rats, inducement of heme oxygenase-1 gene expression in scurvy-prone ODS rats, and the effect of ascorbic acid deficiency on hepatic CYP.

We map 114 gene gains and 74 gene losses in the P450 gene family across the phylogeny of 12 Drosophila species by examining the congruence of gene trees and species trees. Although the number of P450 genes varies from 74 to 94 in the species examined, we infer that there were at least 77 P450 genes in the ancestral Drosophila genome. One of the most striking observations in the data set is the elevated loss of P450 genes in the Drosophila sechellia lineage. The gain and loss events are not evenly distributed among the P450 genes—with 30 genes showing no gene gains or losses whereas others show as many as 20 copy number changes among the species examined. The P450 gene clades showing the fewest number of gene gain and loss events tend to be those evolving with the most purifying selection acting on the protein sequences, although there are exceptions, such as the rapid rate of amino acid replacement observed in the single copy phantom (Cyp306a1) gene. Within D. melanogaster, we observe gene copy number polymorphism in ten P450 genes including multiple cases of interparalog chimeras. Nonallelic homologous recombination (NAHR) has been associated with deleterious mutations in humans, but here we provide a second possible example of an NAHR event in insect P450s being adaptive. Specifically, we find that a polymorphic Cyp12a4/Cyp12a5 chimera correlates with resistance to an insecticide. Although we observe such interparalog exchange in our within-species data sets, we have little evidence of it between species, raising the possibility that such events may occur more frequently than appreciated but are masked by subsequent sequence change. [ABSTRACT FROM PUBLISHER]

The species Acerentulus rapoporti Condé, 1963 is redescribed, transferred to genus Andinentulus Tuxen, 1984, and synonymized with Andinentulus ebhei Tuxen, 1984 on the basis of type series. Andinentulus rapoporti (Condé, 1963) comb. nov. is characterized by very long and sword-shaped foretarsal sensillum a' sensillum b that is half the length of sensillum c, presence of additional seta d6 on the head, absence of seta Pla on abdominal tergites I-VI, and short oblong accessory setae on tergites I-VI. The differences between the genus Andinentulus and morphologically similar genera, which have three setae on the abdominal legs, are discussed. A key to South and Central American Acerentomidae species and their distribution in America is provided. The mitochondrial cytochrome oxidase subunit I sequence (barcode) is provided for several specimens of the species and compared with other proturan barcodes with a phylogenetic analysis. [ABSTRACT FROM AUTHOR]

Acetic acid bacteria (AAB) live in sugar rich environments, including food matrices, plant tissues, and the gut of sugar-feeding insects. By comparing the newly sequenced genomes of Asaia platycodi and Saccharibacter sp., symbionts of Anopheles stephensi and Apis mellifera, respectively, with those of 14 other AAB, we provide a genomic view of the evolutionary pattern of this bacterial group and clues on traits that explain the success of AAB as insect symbionts. A specific pre-adaptive trait, cytochrome bo3 ubiquinol oxidase, appears ancestral in AAB and shows a phylogeny that is congruent with that of the genomes. The functional properties of this terminal oxidase might have allowed AAB to adapt to the diverse oxygen levels of arthropod guts. [ABSTRACT FROM AUTHOR]

Motivation: Identifying protein cavities, channels and pockets accessible to ligands is a major step to predict potential protein–ligands complexes. It is also essential for preparation of protein–ligand docking experiments in the context of enzymatic activity mechanism and structure-based drug design.Results: We introduce a new method, implemented in a program named CCCPP, which computes the void parts of the proteins, i.e. cavities, channels and pockets. The present approach is a variant of the alpha shapes method, with the advantage of taking into account the size and the shape of the ligand. We show that the widely used spherical model of ligands is most of the time inadequate and that cylindrical shapes are more realistic. The analysis of the void parts of the protein is done via a network of channels depending on the ligand. The performance of CCCPP is tested with known substrates of cytochromes P450 (CYP) 1A2 and 3A4 involved in xenobiotics metabolism. The test results indicate that CCCPP is able to find pathways to the buried heminic P450 active site even for high molecular weight CYP 3A4 substrates such as two ketoconazoles together, an experimentally observed situation.Availability: Free binaries are available through a software repository at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.htmlContact: michel.petitjean@univ-paris-diderot.fr [ABSTRACT FROM AUTHOR]

The article discusses role of Bradyrhizobium elkanii (B. elkanii), species of nitrogen-fixing bacterium and related strains in degradation of methoxychlor in soil and surface water environment. Topics discussed include degradation of methoxychlor by B. elkanii (USDA94) species, identification of microbial degraded pesticides and isolation of two strains, Bradyrhizobium sp. 4-1 and 17-4. It also mentions that bradyrhizobium consists of large number of cytochrome P450 genes.

Numerous hypotheses have been proposed for the historical processes governing the rich endemism of Madagascar's biodiversity. The 'watershed model' suggests that drier climates in the recent geological past have resulted in the contraction of forests around major watersheds, thereby defining areas of endemism. We test whether this hypothesis explains phylogeographical patterns in a dry forest-dependent rodent, E liurus myoxinus, an endemic species widely distributed through western Madagascar. We sequenced the mitochondrial cytochrome b locus and nuclear introns of the β-fibrinogen and the growth hormone receptor genes for E. myoxinus. Using a parametric bootstrapping approach, we tested whether the mitochondrial gene tree data fit expectations of local differentiation given the watershed model. We additionally estimated population differentiation and historical demographic parameters, and reconstructed the spatial history of E. myoxinus to highlight spatial and temporal patterns of differentiation. The data do not support the watershed model as a clear explanation for the genetic patterns of diversity within extant E. myoxinus populations. We find striking patterns of latitudinal genetic structure within western Madagascar, and indicate possible roles for environmental and ecological gradients along this axis in generating phylogeographical diversity. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110, 500-517. [ABSTRACT FROM AUTHOR]

Objectives This paper was to clarify the reasons of low bioavailability of vitexin-4″- O-glucoside ( VOG) in rats via hepatic combined with gastrointestinal first-pass effect. Methods Observed the hepatic first-pass effect through the comparison of area under the plasma concentration-time curve from zero to infinity ( AUC0→∞) of VOG in arterial plasma after femoral and portal vein administration (10 mg/kg), similarly, evaluated the gastrointestinal first-pass effect after portal vein (10 mg/kg) and gastrointestinal administration (20 mg/kg). For the study on regulatory mechanisms of cytochrome P450 3 A ( CYP3A) and P-glycoprotein ( P-gp) on the bioavailability of VOG, the solution of verapamil hydrochloride (60 mg/kg) was instilled into intestine at 10 min before the infusion of VOG. Key findings The bioavailability of VOG after intraportal, intestinal as well as gastric administration was 45.1%, 8.1% and 9.8%, respectively. The value of AUC0→∞ for verapamil group was approximately 1.4-fold higher than that for normal saline group, meaning that perhaps CYP3A participated in the metabolism of VOG or P-gp transported VOG outside. Conclusions The hepatic and intestinal first-pass effect were considered to mostly contribute to the low bioavailability of VOG in rats, and the gastric first-pass effect should be neglected. Also, the contribution of CYP3A to metabolism and P-gp mediated efflux have played a significant role in low bioavailability of VOG. [ABSTRACT FROM AUTHOR]

We determined the phylogenetic relationships, population history, and hierarchical structure of genetic variation in pocket gophers distributed on the Baja California Peninsula ( BCP), based on extensive geographic sampling. Using a fragment of the mitochondrial gene cytochrome b (cyt b), we found three latitudinal structured geographic clades (northern, central, and southern). The northern clade occurs in the border area of the USA and the north of BCP, the central clade occurs from the peninsular highlands through the Central Desert of Baja California, and the southern clade is distributed south of the San Ignacio Lagoon. AMOVA showed that genetic variation is higher among clades (64%) than within populations (18.1%). The deepest divergence among clades is very shallow (∼300 000 years), which suggests that climatic changes during the Pleistocene or some inhospitable habitats have affected the structure of this group, rather than influences from older marine transgressions. Phylogenetic groups disclosed by our results do not coincide with the current infraspecific classification; therefore, we propose a change of epithet for BCP gophers ( Thomomys nigricans) and a new subspecific taxonomic arrangement with four subspecies: Thomomys nigricans anitae, Thomomys nigricans martirensis, Thomomys nigricans nigricans, and Thomomys nigricans russeolus. © 2013 The Linnean Society of London [ABSTRACT FROM AUTHOR]

Tris(1-chloro-2-propyl) phosphate (TCPP) and tris(1,3-dichloro-2-propyl) phosphate (TDCPP) are organic flame retardants detected in the environment and biota for which avian toxicological data are limited. In this study, domestic chicken eggs were injected with TCPP or TDCPP (maximum dose = 51,600 and 45,000ng/g egg, respectively) to determine dose-dependent effects on pipping success, development, hepatic messenger RNA (mRNA) expression levels of genes associated with xenobiotic metabolism and the thyroid hormone (TH) pathway, and TH levels following 20–22 days of incubation. Neither compound reduced pipping success; however, TCPP significantly delayed pipping at 9240 and 51,600ng/g and reduced tarsus length at 51,600ng/g. TDCPP exposure resulted in significant decreases in head plus bill length, embryo mass, and gallbladder size at 45,000ng/g and reduced plasma free T4 levels at 7640ng/g. Type I deiodinase, liver fatty acid-binding protein, and cytochrome P450 (CYP) 3A37 mRNA levels were significantly induced by TCPP, whereas TDCPP induced CYP3A37 and CYP2H1. Chemical analysis of egg contents at incubation days 0, 5, 11, 18, and 19 revealed that > 92% of the injected TCPP or TDCPP concentration was detectable up to day 5; however, < 1% was detected by day 19. The observed phenotypic responses to TCPP and TDCPP exposure may be associated with disruption of the TH axis, which is critical for normal growth and development in birds. The effects of TDCPP on the gallbladder indicate that the disturbance of lipid metabolism is a likely mechanism of toxicity. [ABSTRACT FROM AUTHOR]

Copper-containing nitrite reductases (CuNiRs), which catalyse the reversible one-electron reduction of nitrite to nitric oxide, are members of a large family of multi-copper enzymes that require an interprotein electron transfer (ET) reaction with redox partner proteins. Here, we show that the naturally fused type of CuNiR tethering a cytochrome c (Cyt c) at the C-terminus folds as a unique trimeric domain-swapped structure and has a self-sufficient electron flow system. The C-terminal Cyt c domain is located at the surface of the type 1 copper (T1Cu) site in the N-terminal CuNiR domain from the adjacent subunit, the heme-to-Cu distance (10.6 Å) of which is comparable to the transient ET complex of normal CuNiR with Cyt c. The structural aspects for the domain–domain interface and the ET kinetics indicate that the Cyt c–CuNiR domain interaction should be highly transient. The further electrochemical analysis of the interprotein ET reaction with a cognate redox partner protein suggested that an electron is directly transferred from the partner to the T1Cu. Structural and mechanistic comparisons of Cyt c–CuNiR with another cupredoxin-tethering CuNiR highlight the behaviours of extra domains on the fusion types of CuNiRs required for ET through proteins. [ABSTRACT FROM AUTHOR]

The H2-dependent methylene-tetrahydromethanopterin dehydrogenase ( Hmd), also known as the [ Fe]-hydrogenase, is found only in methanogens without cytochromes. In contrast to the binuclear metal centers of the [ Ni Fe]- and [ Fe Fe]-hydrogenases, the [ Fe]-hydrogenase contains only a single Fe atom, which is coordinated by a novel guanylylpyridinol cofactor in the active site. The biosynthesis of the cofactor is not well understood and the responsible genes are unknown. However, seven genes ( hmd co-occurring genes, hcg) encoding proteins of unknown function are always associated with the hmd gene. In the model methanogen Methanococcus maripaludis, we used a genetic background in which a deletion of hmd had a distinct growth phenotype, and made null-mutations in each hcg gene as well as in a gene encoding the Hmd paralog Hmd II, which is hypothesized to function as a scaffold for cofactor synthesis. Deletions in all seven hcg genes resulted in the same growth phenotype as a deletion in hmd, suggesting they are required for Hmd function. In all cases, genetic complementation of the mutation restored the wild-type phenotype. A deletion in hmdII had no effect. [ABSTRACT FROM AUTHOR]

Aim In this work, phenotypic analyses of a Ensifer meliloti fixN1 mutant under free-living and symbiotic conditions have been carried out. Methods and Results Ensifer meliloti fixN1 mutant showed a defect in growth as well as in TMPD-dependent oxidase activity when cells were incubated under micro-oxic conditions. Furthermore, haem c staining analyses of a fixN1 and a fixP1 mutant identified two membrane-bound c-type cytochromes of 27 and 32 kDa, present in microaerobically grown cells and in bacteroids, as the FixO and FixP components of the E. meliloti cbb3 oxidase. Under symbiotic conditions, fixN1 mutant showed a clear nitrogen fixation defect in alfalfa plants that were grown in an N-free nutrient solution during 3 weeks. However, in plants grown for a longer period, fixNOQP1 copy was not indispensable for symbiotic nitrogen fixation. Conclusions The copy 1 of the fix NOQP operon is involved in E. meliloti respiration and growth under micro-oxic conditions as well as in the expression of the FixO and FixP components of the cbb3 oxidase present in free-living microaerobic cultures and in bacteroids. This copy is important for nitrogen fixation during the early steps of the symbiosis. Significance and Impact of the Study It is the first time that a functional analysis of the E. meliloti copy 1 of the fix NOQP operon is performed. In this work, the cytochromes c that constitute the cbb3 oxidase operating in free-living micro-oxic cultures and in bacteroids of E. meliloti have been identified. [ABSTRACT FROM AUTHOR]

Within the species-rich European harvestman genus Trogulus Latreille, 1802, the Balkan Trogulus torosus species-group as defined by Schönhofer and Martens is revised. The group is remarkable because it includes the world's largest Opiliones species, Trogulus torosus Simon, 1885, and Trogulus ozimeci sp. nov. is the first member of the family showing obvious adaption to subterranean life. According to nuclear 28S and mitochondrial cytochrome b gene data, the T. torosus species-group and the Trogulus hirtus species-group form a monophyletic unit. Only the former is treated here as a paraphyletic group. Despite this paraphyly, the T. torosus species-group members share a number of morphological, morphometric, geographical, and ecological traits and are treated here as a unit for revisional work. Morphometric data are shown to be not only useful for species discrimination but also for species-group delineation. Within the T. torosus species-group six species are recognized: Trogulus banaticus Avram, 1971, Trogulus setosissimus Roewer, 1940, and T. torosus are re-described; Trogulus megaligrava sp. nov., T. ozimeci sp. nov., and Trogulus tenuitarsus sp. nov. are described as new. Unusually within Trogulus, strong affiliations with subterranean habitats exist and are discussed. © 2013 The Linnean Society of London [ABSTRACT FROM AUTHOR]

The utility of the cytochrome oxidase I (COI) DNA sequence used for DNA barcoding and a Sequence Characterized Amplified Region for diagnosing boll weevil, Anthonomus grandis Boheman, variants was evaluated. Maximum likelihood analysis of COI DNA sequences from 154 weevils collected from the United States and Mexico supports previous evidence for limited gene flow between weevil populations on wild cotton and commercial cotton in northern Mexico and southern United States. The wild cotton populations represent a variant of the species called the thurberia weevil, which is not regarded as a significant pest. The 31 boll weevil COI haplotypes observed in the study form two distinct haplogroups (A and B) that are supported by five fixed nucleotide differences and a phylogenetic analysis. Although wild and commercial cotton populations are closely associated with specific haplogroups, there is not a fixed difference between the thurberia weevil variant and other populations. The Sequence Characterized Amplified Region marker generated a larger number of inconclusive results than the COI gene but also supported evidence of shared genotypes between wild and commercial cotton weevil populations. These methods provide additional markers that can assist in the identification of pest weevil populations but not definitively diagnose samples. [ABSTRACT FROM AUTHOR]

Five field populations of Diaphorina citri Kuwayama from various regions of Florida were evaluated in 2011 for resistance to commonly used insecticides. Three diagnostic doses (LD50, LD75, and LD95), developed in 2009 using a laboratory susceptible population, were used to measure changes in susceptibility levels of field-collected populations as compared with a susceptible laboratory population. Further reductions in the susceptibility levels of D. citri to chlorpyriphos and fenpropathrin were determined, compared with results obtained in 2010. Mean percent mortality obtained from all five locations was significantly lower than observed with the laboratory susceptible population for all insecticides tested. Previously, expression of five CYP4 genes was implicated in contributing to insecticide metabolism in D. citri. In the current study, we compared the relative expression of these five CYP4 genes and their associated levels of protein expression among field-collected and laboratory susceptible populations. Expression of all CYP4 genes investigated was higher in field-collected populations when normalized against the laboratory susceptible population. There was an increased signal of a band corresponding to a 45 kDa protein in four of the five field populations as measured by the Western blot assay, which suggests increased production of cytochrome P450 enzymes. The current results indicate that insecticide resistance continues to increase in Florida populations of D. citri, particularly to chlorpyriphos and fenpropathrin. However, there was no further decrease in susceptibility of Florida populations of D. citri to neonicotinoid insecticides in 2011 as compared with previous years. [ABSTRACT FROM AUTHOR]