Massive Loss of Olfactory Receptors But Not Trace Amine-Associated Receptors in the World's Deepest-Living Fish (Pseudoliparis swirei)

Olfactory receptor repertoires show highly dynamic evolution associated with ecological adaptations in different species. The Mariana snailfish (Pseudoliparis swirei) living below a depth of 6000 m in the Mariana Trench evolved degraded vision and occupies a specific feeding habitat in a dark, low-food environment. However, whether such adaptations involve adaptive changes in the chemosensory receptor repertoire is not known. Here, we conducted a comparative analysis of the olfactory receptor (OR) and trace amine-associated receptor (TAAR) gene repertoires in nine teleosts with a focus on the evolutionary divergence between the Mariana snailfish and its shallow-sea relative, Tanaka's snailfish (Liparis tanakae). We found many fewer functional OR genes and a significantly higher fraction of pseudogenes in the Mariana snailfish, but the numbers of functional TAAR genes in the two species were comparable. Phylogenetic analysis showed that the expansion patterns of the gene families were shared by the two species, but that Mariana snailfish underwent massive gene losses in its OR repertoire. Despite an overall decreased size in OR subfamilies and a reduced number of TAAR subfamilies in the Mariana snailfish, expansion of certain subfamilies was observed. Selective pressure analysis indicated greatly relaxed selective strength in ORs but a slightly enhanced selective strength in TAARs of Mariana snailfish. Overall, our study reveals simplified but specific OR and TAAR repertoires in the Mariana snailfish shaped by natural selection with respect to ecological adaptations in the hadal environment. This is the first study on the chemosensation evolution in vertebrates living in the hadal zone, which could provide new insights into evolutionary adaptation to the hadal environment

Ancient duplications and functional divergence in the interferon regulatory factors of vertebrates provide insights into the evolution of vertebrate immune systems

Interferon regulatory factors (IRFs) were first discovered as transcription factors that regulate the transcription of human interferon (IFN)-beta. Increasing evidence shows that they might be important players involved in Adaptive immune system (AIS) evolution. Although numbers of IRFs have been identified in chordates, the evolutionary history and functional diversity of this gene family during the early evolution of vertebrates have remained obscure. Using IRF HMM profile and HMMER searches, we identified 148 IRFs in 11 vertebrates and 4 protochordates. For them, we reconstructed the phylogenetic relationships, determined the synteny conservation, investigated the profile of natural selection, and analyzed the expression patterns in four &quot;living fossil&quot; vertebrates: lamprey, elephant shark, coelacanth and bichir. The results from phylogeny and synteny analysis imply that vertebrate IRFs evolved from three predecessors, instead of four as suggested in a previous study, as results from an ancient duplication followed by special expansions and lost during the vertebrate evolution. The profile of natural selection and expression reveals functional dynamics during the process. Together, they suggest that the 2nd whole-genome duplication (2WGD) provided raw materials for innovation in the IRF family, and that the birth of type-I IFN might be an important factor inducing the establishment of IRF-mediated immune networks. As a member involved in the AIS evolution, IRF provide insights into the process and mechanism involved in the complexity and novelties of vertebrate immune systems. (C) 2017 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.</p

Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

AbstractBackgroundPolypterus senegalus can fully regenerate its pectoral lobed fins, including a complex endoskeleton, with remarkable precision. However, despite the enormous potential of this species for use in medical research, its regeneration mechanisms remain largely unknown.MethodsTo identify the differentially expressed proteins (DEPs) during the early stages of lobed fin regeneration in P. senegalus, we performed a differential proteomic analysis using isobaric tag for relative and absolute quantitation (iTRAQ) approach based quantitative proteome from the pectoral lobed fins at 3 time points. Furthermore, we validated the changes in protein expression with multiple-reaction monitoring (MRM) analysis.ResultsThe experiment yielded a total of 3177 proteins and 15,091 unique peptides including 1006 non-redundant (nr) DEPs. Of these, 592 were upregulated while 349 were downregulated after lobed fin amputation when compared to the original tissue. Bioinformatics analyses showed that the DEPs were mainly associated with Ribosome and RNA transport, metabolic, ECM-receptor interaction, Golgi and endoplasmic reticulum, DNA replication, and Regulation of actin cytoskeleton.ConclusionsTo our knowledge, this is the first proteomic research to investigate alterations in protein levels and affected pathways in bichirs&rsquo; lobe-fin/limb regeneration. In addition, our study demonstrated a highly dynamic regulation during lobed fin regeneration in P. senegalus. These results not only provide a comprehensive dataset on differentially expressed proteins during the early stages of lobe-fin/limb regeneration but also advance our understanding of the molecular mechanisms underlying lobe-fin/limb regeneration.</p

Aerobic Synthesis of Substituted Quinoline from Aldehyde and Aniline: Copper-Catalyzed Intermolecular C–H Active and C–C Formative Cyclization

An efficient method for the direct synthesis of substituted quinolines from anilines and aldehydes through C–H functionalization, C–C/C–N bond formation, and C–C bond cleavage has been developed. The method is simple and practical and employs air as an oxidant

Epidemiology of carbapenem-resistant Klebsiella pneumoniae bloodstream infections after renal transplantation from donation after cardiac death in a Chinese hospital: a case series analysis

Abstract Background Although the high mortality rates have been extensively reported worldwide, few studies have investigated the epidemiology of CRKP-BSIs in the early stage after kidney transplantation (KTx) from donation after cardiac death (DCD). We sought to describe the epidemiological and clinical characteristics of cases of carbapenem resistant Klebsiella pneumoniae bloodstream infections (CRKP-BSIs) in kidney transplantation recipients (KTRs) from DCD in our hospital. Methods A retrospective analysis of clinical data of CRKP-BSIs in KTRs admitted to a Chinese hospital in Beijing, China, between January 1, 2012 and December 31, 2016 was performed. The annual percentage of patients with CRKP, the annual number of total KTRs and KTRs from DCD were determined. The genetic relatedness of the strains was determined by polymerase chain reaction and pulse field gel electrophoresis (PFGE). Results During the study period, there were total 947 KTRs in our hospital, including 275 KTRs from DCD. Five incidences of CRKP-BSIs in KTRs were identified, and two of them (Case 1,3) from the same foreign hospital. The incidence of CRKP-BSIs in the early stage (within 3 months) following kidney transplantation (KTx) from DCD was about 1.1% (3/275). In Case 1–3 and 5, the rupture of renal transplant artery was presented on the 40th, 16th, 43th and 74th day after KTx, and in Case 4, the thrombus of renal transplant artery was presented on the 13th day after KTx. Three cases (Case 1,2,5) occurring pneumothorax on the 45th, 51th and 32th day after KTx. Four cases (Case 1–4) received the excision of the transplanted kidney for the treatment. Polymerase chain reaction showed the bands for case 2 were distinctive from other cases. Pulse field gel electrophoresis showed mainly three clusters of the bands for all the isolates. Conclusions During the study period, we observed an increase in the occurrence of CRKP-BSIs among KTRs from DCD in our hospital. We demonstrated that rupture/thrombus of the renal transplant artery was associated with CRKP-BSI in the early stage after KTx from DCD. Albeit the low incidence of CRKP-BSI (1.1%) after KTx from DCD, the high mortality (4/5) had been observed from the prognosis of the patients. Thorough surveillance of DCD donors, early identification of CRKP-BSI, necessary preventative measurements and use of appropriate treatments should be the strategy for CRKP-BSI in the early stage after KTx from DCD

I₂‑Mediated Oxidative Cyclization for Synthesis of Substituted Indolizines

A direct method for the synthesis of substituted indolizines by means of I₂-mediated oxidative tandem cyclization via C–N/C–C bond formation was developed. Various substituted aromatic/aliphatic enolizable aldehydes and 2-pyridylacetates/acetonitrile/acetone proceeded smoothly in this transformation, and the desired products were generated in moderate to good yields

Iodine-Mediated Thiolation of Substituted Naphthols/Naphthylamines and Arylsulfonyl Hydrazides via C(sp²)–H Bond Functionalization

A direct method has been developed for iodine-mediated thiolation of naphthols/naphthylamines and arylsulfonyl hydrazides through the formation of C–S bond and cleavage of S–N/S–O bonds. In this transformation, a range of valuable thioethers are easily achieved in moderate to good yields

I₂‑Catalyzed Synthesis of Substituted Pyrroles from α‑Amino Carbonyl Compounds and Aldehydes

A direct method for the synthesis of 1,3,4-triarylpyrroles was achieved easily from cyclization of α-amino carbonyl compounds and aldehydes catalyzed by I₂. Various substituted groups can be employed, and this reaction can proceed smoothly in moderate to good yields