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Microbiology
Antibodies from a Human Survivor Define Sites of Vulnerability for Broad Protection against Ebolaviruses
May 19, 2017   Cell
Wec AZ, Herbert AS, Murin CD, Nyakatura EK, Abelson DM,   . . . . . .   , Walker LM, Ward AB, Dye JM, Chandran K, Bornholdt ZA
Antibodies from a Human Survivor Define Sites of Vulnerability for Broad Protection against Ebolaviruses
May 19, 2017
Cell
Experimental monoclonal antibody (mAb) therapies have shown promise for treatment of lethal Ebola virus (EBOV) infections, but their species-specific recognition of the viral glycoprotein (GP) has limited their use against other divergent ebolaviruses associated with human disease. Here, we mined the human immune response to natural EBOV infection and identified mAbs with exceptionally potent pan-ebolavirus neutralizing activity and protective efficacy against three virulent ebolaviruses. These mAbs recognize an inter-protomer epitope in the GP fusion loop, a critical and conserved element of the viral membrane fusion machinery, and neutralize viral entry by targeting a proteolytically primed, fusion-competent GP intermediate (GPCL) generated in host cell endosomes. Only a few somatic hypermutations are required for broad antiviral activity, and germline-approximating variants display enhanced GPCL recognition, suggesting that such antibodies could be elicited more efficiently with suitably optimized GP immunogens. Our findings inform the development of both broadly effective immunotherapeutics and vaccines against filoviruses. Copyright © 2017 Elsevier Inc. All rights reserved.
Immunization-Elicited Broadly Protective Antibody Reveals Ebolavirus Fusion Loop as a Site of Vulnerability
May 19, 2017   Cell
Zhao X, Howell KA, He S, Brannan JM, Wec AZ,   . . . . . .   , Chandran K, Dye JM, Qiu X, Li Y, Aman MJ
Immunization-Elicited Broadly Protective Antibody Reveals Ebolavirus Fusion Loop as a Site of Vulnerability
May 19, 2017
Cell
While neutralizing antibodies are highly effective against ebolavirus infections, current experimental ebolavirus vaccines primarily elicit species-specific antibody responses. Here, we describe an immunization-elicited macaque antibody (CA45) that clamps the internal fusion loop with the N terminus of the ebolavirus glycoproteins (GPs) and potently neutralizes Ebola, Sudan, Bundibugyo, and Reston viruses. CA45, alone or in combination with an antibody that blocks receptor binding, provided full protection against all pathogenic ebolaviruses in mice, guinea pigs, and ferrets. Analysis of memory B cells from the immunized macaque suggests that elicitation of broadly neutralizing antibodies (bNAbs) for ebolaviruses is possible but difficult, potentially due to the rarity of bNAb clones and their precursors. Unexpectedly, germline-reverted CA45, while exhibiting negligible binding to full-length GP, bound a proteolytically remodeled GP with picomolar affinity, suggesting that engineered ebolavirus vaccines could trigger rare bNAb precursors more robustly. These findings have important implications for developing pan-ebolavirus vaccine and immunotherapeutic cocktails. Copyright © 2017 Elsevier Inc. All rights reserved.
The U6 snRNA m6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention
May 19, 2017   Cell
Pendleton KE, Chen B, Liu K, Hunter OV, Xie Y, Tu BP, Conrad NK
The U6 snRNA m6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention
May 19, 2017
Cell
Maintenance of proper levels of the methyl donor S-adenosylmethionine (SAM) is critical for a wide variety of biological processes. We demonstrate that the N6-adenosine methyltransferase METTL16 regulates expression of human MAT2A, which encodes the SAM synthetase expressed in most cells. Upon SAM depletion by methionine starvation, cells induce MAT2A expression by enhanced splicing of a retained intron. Induction requires METTL16 and its methylation substrate, a vertebrate conserved hairpin (hp1) in the MAT2A 3' UTR. Increasing METTL16 occupancy on the MAT2A 3' UTR is sufficient to induce efficient splicing. We propose that, under SAM-limiting conditions, METTL16 occupancy on hp1 increases due to inefficient enzymatic turnover, which promotes MAT2A splicing. We further show that METTL16 is the long-unknown methyltransferase for the U6 spliceosomal small nuclear RNA (snRNA). These observations suggest that the conserved U6 snRNA methyltransferase evolved an additional function in vertebrates to regulate SAM homeostasis. Copyright © 2017 Elsevier Inc. All rights reserved.
Ebolavirus's Foibles
May 19, 2017   Cell
Yamayoshi S, Kawaoka Y
Ebolavirus's Foibles
May 19, 2017
Cell
Ebola virus disease poses a global health threat. Here, two studies by Wec et al. and Zhao et al. identified vulnerability in an internal fusion loop of an ebolavirus glycoprotein. Monoclonal antibodies elicited from immunization and isolated from a human survivor that recognized epitopes in this area neutralized all five ebolaviruses, guiding the development of a pan-ebolavirus immunotherapy. Copyright © 2017 Elsevier Inc. All rights reserved.
Big Questions in Microbiology
May 19, 2017   Cell
Dengue Antibodies, then Zika: A Fatal Sequence in Mice
May 17, 2017   Immunity
Miner JJ, Diamond MS
Dengue Antibodies, then Zika: A Fatal Sequence in Mice
May 17, 2017
Immunity
Anti-Dengue virus (DENV) antibodies can be either protective or pathogenic in humans with prior DENV infection. In a recent issue of Science, Bardina et al. (2017) demonstrated that passive transfer of immune plasma against DENV and West Nile virus (WNV) can enhance Zika virus (ZIKV) infection and pathogenesis in mice. Copyright © 2017 Elsevier Inc. All rights reserved.
Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes
May 17, 2017   Nature Add nature.com free-link Cancel
Liu Y, Liu J, Du S, Shan C, Nie K, Zhang R, Li XF, Zhang R, Wang T, Qin CF, Wang P, Shi PY, Cheng G
Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes
May 17, 2017
Nature
Zika virus (ZIKV) remained obscure until the recent explosive outbreaks in French Polynesia (2013-2014) and South America (2015-2016). Phylogenetic studies have shown that ZIKV has evolved into African and Asian lineages. The Asian lineage of ZIKV was responsible for the recent epidemics in the Americas. However, the underlying mechanisms through which ZIKV rapidly and explosively spread from Asia to the Americas are unclear. Non-structural protein 1 (NS1) facilitates flavivirus acquisition by mosquitoes from an infected mammalian host and subsequently enhances viral prevalence in mosquitoes. Here we show that NS1 antigenaemia determines ZIKV infectivity in its mosquito vector Aedes aegypti, which acquires ZIKV via a blood meal. Clinical isolates from the most recent outbreak in the Americas were much more infectious in mosquitoes than the FSS13025 strain, which was isolated in Cambodia in 2010. Further analyses showed that these epidemic strains have higher NS1 antigenaemia than the FSS13025 strain because of an alanine-to-valine amino acid substitution at residue 188 in NS1. ZIKV infectivity was enhanced by this amino acid substitution in the ZIKV FSS13025 strain in mosquitoes that acquired ZIKV from a viraemic C57BL/6 mouse deficient in type I and II interferon (IFN) receptors (AG6 mouse). Our results reveal that ZIKV evolved to acquire a spontaneous mutation in its NS1 protein, resulting in increased NS1 antigenaemia. Enhancement of NS1 antigenaemia in infected hosts promotes ZIKV infectivity and prevalence in mosquitoes, which could have facilitated transmission during recent ZIKV epidemics.
uORF-mediated translation allows engineered plant disease resistance without fitness costs
May 17, 2017   Nature Add nature.com free-link Cancel
Xu G, Yuan M, Ai C, Liu L, Zhuang E, Karapetyan S, Wang S, Dong X
uORF-mediated translation allows engineered plant disease resistance without fitness costs
May 17, 2017
Nature
Controlling plant disease has been a struggle for humankind since the advent of agriculture. Studies of plant immune mechanisms have led to strategies of engineering resistant crops through ectopic transcription of plants' own defence genes, such as the master immune regulatory gene NPR1 (ref. 1). However, enhanced resistance obtained through such strategies is often associated with substantial penalties to fitness, making the resulting products undesirable for agricultural applications. To remedy this problem, we sought more stringent mechanisms of expressing defence proteins. On the basis of our latest finding that translation of key immune regulators, such as TBF1 (ref. 3), is rapidly and transiently induced upon pathogen challenge (see accompanying paper), we developed a 'TBF1-cassette' consisting of not only the immune-inducible promoter but also two pathogen-responsive upstream open reading frames (uORFsTBF1) of the TBF1 gene. Here we demonstrate that inclusion of uORFsTBF1-mediated translational control over the production of snc1-1 (an autoactivated immune receptor) in Arabidopsis thaliana and AtNPR1 in rice enables us to engineer broad-spectrum disease resistance without compromising plant fitness in the laboratory or in the field. This broadly applicable strategy may lead to decreased pesticide use and reduce the selective pressure for resistant pathogens.
Global translational reprogramming is a fundamental layer of immune regulation in plants
May 17, 2017   Nature Add nature.com free-link Cancel
Xu G, Greene GH, Yoo H, Liu L, Marqués J, Motley J, Dong X
Global translational reprogramming is a fundamental layer of immune regulation in plants
May 17, 2017
Nature
In the absence of specialized immune cells, the need for plants to reprogram transcription to transition from growth-related activities to defence is well understood. However, little is known about translational changes that occur during immune induction. Using ribosome footprinting, here we perform global translatome profiling on Arabidopsis exposed to the microbe-associated molecular pattern elf18. We find that during this pattern-triggered immunity, translation is tightly regulated and poorly correlated with transcription. Identification of genes with altered translational efficiency leads to the discovery of novel regulators of this immune response. Further investigation of these genes shows that messenger RNA sequence features are major determinants of the observed translational efficiency changes. In the 5' leader sequences of transcripts with increased translational efficiency, we find a highly enriched messenger RNA consensus sequence, R-motif, consisting of mostly purines. We show that R-motif regulates translation in response to pattern-triggered immunity induction through interaction with poly(A)-binding proteins. Therefore, this study provides not only strong evidence, but also a molecular mechanism, for global translational reprogramming during pattern-triggered immunity in plants.
Inactivated influenza virus vaccines: the future of TIV and QIV
May 15, 2017   Current Opinion In Virology
Schotsaert M, García-Sastre A
Inactivated influenza virus vaccines: the future of TIV and QIV
May 15, 2017
Current Opinion In Virology
Influenza viruses continue to be a major public health concern, despite the availability of vaccines. Currently licensed influenza vaccines aim at the induction of antibodies that target hemagglutinin, the major antigenic determinant on the surface of influenza virions that is responsible for attachment of the virus to the host cell that is to be infected. Currently licensed influenza vaccines come as inactivated or live attenuated influenza vaccines and are trivalent or quadrivalent as they contain antigens of two influenza A and one or two influenza B strains that circulate in the human population, respectively. In this review we briefly compare trivalent and quadrivalent inactivated influenza vaccines (TIV and QIV) with live attenuated influenza vaccines (LAIV). The use of the latter vaccine type in children age 2-8 has been disrecommended recently by the American Centers for Disease Control and Prevention due to inferior vaccine effectiveness in this age group in recent seasons. This recommendation will favor the use of TIV and QIV over LAIV in the near future. However, there is much evidence from studies in humans that illustrate the benefit of LAIV and we discuss some of the mechanisms that contribute to broader protection against influenza viruses of different subtypes induced by natural infection and LAIV. The future challenge will be to apply these insights to allow induction of broader and long-lasting protection provided by TIV and QIV vaccines, for example, by the use of adjuvants or combining LAIV with TIV and QIV. Other immune factors than serum hemagglutination inhibiting antibodies have shown to correlate with protection provided by TIV and QIV, which illustrates the need for other correlates of protection than hemagglutination inhibition by serum antibodies and justifies more focus on influenza antigens in the TIV and QIV other than hemagglutinin. Copyright © 2017 Elsevier B.V. All rights reserved.
Metabolic Phenotypes of Response to Vaccination in Humans
May 15, 2017   Cell
Li S, Sullivan NL, Rouphael N, Yu T, Banton S,   . . . . . .   , Mulligan MJ, Nakaya HI, Levin M, Ahmed R, Pulendran B
Metabolic Phenotypes of Response to Vaccination in Humans
May 15, 2017
Cell
Herpes zoster (shingles) causes significant morbidity in immune compromised hosts and older adults. Whereas a vaccine is available for prevention of shingles, its efficacy declines with age. To help to understand the mechanisms driving vaccinal responses, we constructed a multiscale, multifactorial response network (MMRN) of immunity in healthy young and older adults immunized with the live attenuated shingles vaccine Zostavax. Vaccination induces robust antigen-specific antibody, plasmablasts, and CD4+ T cells yet limited CD8+ T cell and antiviral responses. The MMRN reveals striking associations between orthogonal datasets, such as transcriptomic and metabolomics signatures, cell populations, and cytokine levels, and identifies immune and metabolic correlates of vaccine immunity. Networks associated with inositol phosphate, glycerophospholipids, and sterol metabolism are tightly coupled with immunity. Critically, the sterol regulatory binding protein 1 and its targets are key integrators of antibody and T follicular cell responses. Our approach is broadly applicable to study human immunity and can help to identify predictors of efficacy as well as mechanisms controlling immunity to vaccination. Copyright © 2017 Elsevier Inc. All rights reserved.
Tracing the Enterococci from Paleozoic Origins to the Hospital
May 15, 2017   Cell
Lebreton F, Manson AL, Saavedra JT, Straub TJ, Earl AM, Gilmore MS
Tracing the Enterococci from Paleozoic Origins to the Hospital
May 15, 2017
Cell
We examined the evolutionary history of leading multidrug resistant hospital pathogens, the enterococci, to their origin hundreds of millions of years ago. Our goal was to understand why, among the vast diversity of gut flora, enterococci are so well adapted to the modern hospital environment. Molecular clock estimation, together with analysis of their environmental distribution, phenotypic diversity, and concordance with host fossil records, place the origins of the enterococci around the time of animal terrestrialization, 425-500 mya. Speciation appears to parallel the diversification of hosts, including the rapid emergence of new enterococcal species following the End Permian Extinction. Major drivers of speciation include changing carbohydrate availability in the host gut. Life on land would have selected for the precise traits that now allow pathogenic enterococci to survive desiccation, starvation, and disinfection in the modern hospital, foreordaining their emergence as leading hospital pathogens. Copyright © 2017 Elsevier Inc. All rights reserved.
Higher viral load and genetic diversity of HIV-1 in the seminal compartments than in the blood of seven Chinese homosexual men with early HIV-1 infection
May 13, 2017   Microbiology And Immunology
Jiao YM, Chen GL, Zhu WJ, Huang HH, Fu JL, Chen WW, Shi M, Zhang T, Wu H, Wang FS
Higher viral load and genetic diversity of HIV-1 in the seminal compartments than in the blood of seven Chinese homosexual men with early HIV-1 infection
May 13, 2017
Microbiology And Immunology
To date, there have been no reports characterizing the Human Immunodeficiency Virus-1 (HIV-1) in the semen of Chinese men having sex with men (MSM) with early infection of HIV-1.We examined genetic diversity and viral load of HIV-1 in the seminal compartments and blood of Chinese MSM with early HIV-1 infection in this study. Viral load and genetic diversity of HIV-1 in paired samples of semen and blood were analyzed in seven homosexual patients who were with early HIV-1 infection. Levels of HIV-1 RNA and DNA were tested by real-time PCR assays. Through sequencing the C2-V5 region of the HIV-1 env gene we determined the HIV-1 genotype and genetic diversity based on V3 loop amino acid sequences by using Geno2pheno and PSSM programs theco-receptor usage was predicated. We found that in seminal plasma the HIV-1 RNA levels were higher compared with those in blood plasma and total, the levels of 2-LTR circular and integrated HIV-1 DNA were higher in seminal cells compared with those in peripheral blood mononuclear cells from all seven early HIV-infected patients. There was higher HIV-1 genetic diversity in seminal compartments as compared to blood compartments. HIV-1 in plasma displayed higher genetic diversity than in cells from the blood and semen, respectively. In addition, the V3 loop central motifs, which present some key neutralizing antibodies epitopes, varied between the blood and the semen. So virological parameters in semen may be more representative to evaluate the transmission risk in early HIV infection. © 2017 The Societies and Wiley Publishing Asia Pty Ltd.
Pathological role of anti-CD4 antibodies in HIV-infected immunologic non-responders under viral suppressive antiretroviral therapy
May 12, 2017   The Journal Of Infectious Diseases
Luo Z, Li Z, Martin L, Wan Z, Meissner EG,   . . . . . .   , Wu J, Huang L, Heath SL, Li Z, Jiang W
Pathological role of anti-CD4 antibodies in HIV-infected immunologic non-responders under viral suppressive antiretroviral therapy
May 12, 2017
The Journal Of Infectious Diseases
Increased mortality and morbidity occurs in human immunodeficiency virus (HIV)-infected patients who fail to increase CD4+ T cell counts despite achieving viral suppression with antiretroviral therapy (ART). Here we identified an underlying mechanism. Significantly elevated plasma levels of anti-CD4 IgGs were found in HIV+ immunologic non-responders (CD4+ T cell counts ≤ 350 cells/μl) compared to HIV+ immunologic responders (CD4+ T cell counts ≥ 500 cells/μl) and healthy controls. Higher plasma level of anti-CD4 IgG correlated with blunted CD4+ T cell recovery. Furthermore, purified anti-CD4 IgGs from HIV+ immunologic non-responders induced NK cell-dependent CD4+ T cell cytolysis and apoptosis through antibody-dependent cell-mediated cytotoxicity (ADCC) in vitro. We also found that anti-CD4 IgG-mediated ADCC exerts greater apoptosis on naive relative to memory CD4+ T cells. Consistently, increased frequencies of CD107a+ NK cells and profound decreases of naive CD4+ T cells were observed in immunologic non-responders compared to responders and healthy controls ex vivo. These data indicate that autoreactive anti-CD4 IgGs may play an important role in the blunted CD4+ T cell reconstitution despite effective ART. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.
A ROS-dependent and Caspase-3-mediated apoptosis in sheep bronchial epithelial cells in response to Mycoplasma Ovipneumoniae infections
May 12, 2017   Veterinary Immunology And Immunopathology
Xue D, Li Y, Jiang Z, Deng G, Li M, Liu X, Wang Y
A ROS-dependent and Caspase-3-mediated apoptosis in sheep bronchial epithelial cells in response to Mycoplasma Ovipneumoniae infections
May 12, 2017
Veterinary Immunology And Immunopathology
Mycoplasma Ovipneumoniae (M. ovipneumoniae) is a primary etiological agent of enzootic pneumonia in sheep and goats. It can enter and colonize ovine respiratory epithelial cells to establish an infection, which leads a serious cell death of epithelial cells. However, the nature of the interaction between pathogen of M. ovipneumoniae and host cells in the cell injury is currently not well understood. In this study, we investigated the epithelial cell apoptosis caused by an infection of M. ovipneumoniae in sheep primary air-liquid interface (ALI) epithelial cultures. The results showed that M. ovipneumoniae could specifically bind to ciliated cells at early stage of infection. Flow cytometric analysis demonstrated that an infection of M. ovipneumoniae induced a time-dependent cell apoptotic cell death, accompanied with an increased production of extracellular nitric oxide (NO), intracellular reactive oxygen species (ROS) production and activation of caspase-3 signaling in sheep bronchial epithelial cells. The induced cell apoptosis was further confirmed by a transferase-mediated deoxyuridine triphosphate-biotin nick end-labeling (TUNEL) assay. Interestingly, the M. ovipneumoniae-induced apoptosis and activation of caspase-3 were correlated with the production of ROS but not NO. Mechanistically, M. ovipneumoniae-induced cell apoptosis was mediated by a mechanism by increasing the expression of phosphorylation of p38 and pro-apoptotic proteins, and activating caspase-3, caspase-8 and poly ADP-ribose polymerase (PARP) cleavage. These results suggest a ROS-dependent and caspase-3-mediated cell apoptosis in sheep bronchial epithelial cells in response to M. ovipneumoniae infections. Copyright © 2017. Published by Elsevier B.V.
A Chimeric Egfr Protein Reporter Mouse Reveals Egfr Localization and Trafficking In Vivo
May 12, 2017   Cell Reports
Yang YP, Ma H, Starchenko A, Huh WJ, Li W, Hickman FE, Zhang Q, Franklin JL, Mortlock DP, Fuhrmann S, Carter BD, Ihrie RA, Coffey RJ
A Chimeric Egfr Protein Reporter Mouse Reveals Egfr Localization and Trafficking In Vivo
May 12, 2017
Cell Reports
EGF receptor (EGFR) is a critical signaling node throughout life. However, it has not been possible to directly visualize endogenous Egfr in mice. Using CRISPR/Cas9 genome editing, we appended a fluorescent reporter to the C terminus of the Egfr. Homozygous reporter mice appear normal and EGFR signaling is intact in vitro and in vivo. We detect distinct patterns of Egfr expression in progenitor and differentiated compartments in embryonic and adult mice. Systemic delivery of EGF or amphiregulin results in markedly different patterns of Egfr internalization and trafficking in hepatocytes. In the normal intestine, Egfr localizes to the crypt rather than villus compartment, expression is higher in adjacent epithelium than in intestinal tumors, and following colonic injury expression appears in distinct cell populations in the stroma. This reporter, under control of its endogenous regulatory elements, enables in vivo monitoring of the dynamics of Egfr localization and trafficking in normal and disease states. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
Endothelial TLR4 and the microbiome drive cerebral cavernous malformations
May 10, 2017   Nature Add nature.com free-link Cancel
Tang AT, Choi JP, Kotzin JJ, Yang Y, Hong CC,   . . . . . .   , Morrison L, Kim H, Awad IA, Zheng X, Kahn ML
Endothelial TLR4 and the microbiome drive cerebral cavernous malformations
May 10, 2017
Nature
Cerebral cavernous malformations (CCMs) are a cause of stroke and seizure for which no effective medical therapies yet exist. CCMs arise from the loss of an adaptor complex that negatively regulates MEKK3-KLF2/4 signalling in brain endothelial cells, but upstream activators of this disease pathway have yet to be identified. Here we identify endothelial Toll-like receptor 4 (TLR4) and the gut microbiome as critical stimulants of CCM formation. Activation of TLR4 by Gram-negative bacteria or lipopolysaccharide accelerates CCM formation, and genetic or pharmacologic blockade of TLR4 signalling prevents CCM formation in mice. Polymorphisms that increase expression of the TLR4 gene or the gene encoding its co-receptor CD14 are associated with higher CCM lesion burden in humans. Germ-free mice are protected from CCM formation, and a single course of antibiotics permanently alters CCM susceptibility in mice. These studies identify unexpected roles for the microbiome and innate immune signalling in the pathogenesis of a cerebrovascular disease, as well as strategies for its treatment.
MMPs/TIMPs imbalances in the peripheral blood and cerebrospinal fluid are associated with the pathogenesis of HIV-1-associated neurocognitive disorders
May 10, 2017   Brain, Behavior, And Immunity
Xing Y, Shepherd N, Lan J, Li W, Rane S, Gupta SK, Zhang S, Dong J, Yu Q
MMPs/TIMPs imbalances in the peripheral blood and cerebrospinal fluid are associated with the pathogenesis of HIV-1-associated neurocognitive disorders
May 10, 2017
Brain, Behavior, And Immunity
HIV-1-associated neurocognitive disorders (HAND) continue to be a major concern in the infected population, despite the widespread use of combined antiretroviral therapy (cART). Growing evidence suggests that an imbalance between matrix metalloproteinases (MMPs) and endogenous tissue inhibitors of MMPs (TIMPs) contributes to the pathogenesis of HAND. In our present study, we examined protein levels and enzymatic activities of MMPs and TIMPs in both plasma and cerebrospinal fluid (CSF) samples from HIV-1 patients with or without HAND and HIV-1-negative controls. Imbalances between MMPs and TIMPs with distinct patterns were revealed in both the peripheral blood and CSF of HIV-1 patients, especially those with HAND. In the peripheral blood, the protein levels of MMP-2, MMP-9, TIMP-1, TIMP-2, and the enzymatic activities of MMP-2 and MMP-9 were increased in HIV-1 patients with or without HAND when compared with HIV-1-negative controls. The enzymatic activity of MMP-2, but not MMP-9, was further increased in plasma samples of HAND patients than that of HIV-1 patients without HAND. Notably, the ratio of MMP-2/TIMP-2 in plasma was significantly increased in HAND patients, not in patients without HAND. In the CSF, MMP-2 activity was increased, but the ratio of MMP-2/TIMP-2 was not altered. De novo induction and activation of MMP-9 in the CSF of HAND patients was particularly prominent. The imbalances between MMPs and TIMPs in the blood and CSF were related to the altered profiles of inflammatory cytokines/chemokines and monocyte activation in these individuals. In addition, plasma from HIV-1 patients directly induced integrity disruption of an in vitro blood-brain barrier (BBB) model, leading to increased BBB permeability and robust transmigration of monocytes/macrophages. These results indicate that imbalances between MMPs and TIMPs are involved in BBB disruption and are implicated in the pathogenesis of neurological disorders such as HAND in HIV-1 patients. Copyright © 2017 Elsevier Inc. All rights reserved.
De novo Sequencing and Transcriptome Analysis Reveal Key Genes Regulating Steroid Metabolism in Leaves, Roots, Adventitious Roots and Calli of Periploca sepium Bunge
May 09, 2017   Frontiers In Plant Science
Zhang J, Li X, Lu F, Wang S, An Y, Su X, Li X, Ma L, Han G
De novo Sequencing and Transcriptome Analysis Reveal Key Genes Regulating Steroid Metabolism in Leaves, Roots, Adventitious Roots and Calli of Periploca sepium Bunge
May 09, 2017
Frontiers In Plant Science
Periploca sepium Bunge is a traditional medicinal plant, whose root bark is important for Chinese herbal medicine. Its major bioactive compounds are C21 steroids and periplocin, a kind of cardiac glycoside, which are derived from the steroid synthesis pathway. However, research on P. sepium genome or transcriptomes and their related genes has been lacking for a long time. In this study we estimated this species nuclear genome size at 170 Mb (using flow cytometry). Then, RNA sequencing of four different tissue samples of P. sepium (leaves, roots, adventitious roots, and calli) was done using the sequencing platform Illumina/Solexa Hiseq 2,500. After de novo assembly and quantitative assessment, 90,375 all-transcripts and 71,629 all-unigenes were finally generated. Annotation efforts that used a number of public databases resulted in detailed annotation information for the transcripts. In addition, differentially expressed genes (DEGs) were identified by using digital gene profiling based on the reads per kilobase of transcript per million reads mapped (RPKM) values. Compared with the leaf samples (L), up-regulated genes and down-regulated genes were eventually obtained. To deepen our understanding of these DEGs, we performed two enrichment analyses: gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Here, the analysis focused upon the expression characteristics of those genes involved in the terpene metabolic pathway and the steroid biosynthesis pathway, to better elucidate the molecular mechanism of bioactive steroid synthesis in P. sepium. The bioinformatics analysis enabled us to find many genes that are involved in bioactive steroid biosynthesis. These genes encoded acetyl-CoA acetyltransferase (ACAT), HMG-CoA synthase (HMGS), HMG-CoA reductase (HMGR), mevalonate kinase (MK), phosphomevalonate kinase (PMK), mevalonate diphosphate decarboxylase (MDD), isopentenylpyrophosphate isomerase (IPPI), farnesyl pyrophosphate synthase (FPS), squalene synthase (SS), squalene epoxidase (SE), cycloartenol synthase (CAS), sterol C-24 methyltransferase (SMT1), sterol-4alpha-methyl oxidase 1 (SMO1), sterol 14alpha-demethylase (CYP51/14-SDM), delta(14)-sterol reductase (FK/14SR), C-8,7 sterol isomerase (HYD1), sterol-4alpha-methyl oxidase 2 (SMO2), delta(7)-sterol-C5(6)-desaturase (STE1/SC5DL), 7-dehydrocholesterol reductase (DWF5/DHCR7), delta (24)-sterol reductase (DWF1/DHCR24), sterol 22-desaturase (CYP710A), progesterone 5beta-reductase (5β-POR), 3-beta-hydroxysteroid dehydrogenase (3β-HSD). This research will be helpful to further understand the mechanism of bioactive steroid biosynthesis in P. sepium, namely C21 steroid and periplocin biosynthesis.
Widespread adenine N6-methylation of active genes in fungi
May 08, 2017   Nature Genetics Add nature.com free-link Cancel
Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ,   . . . . . .   , O'Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV
Widespread adenine N6-methylation of active genes in fungi
May 08, 2017
Nature Genetics
N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes, but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in early-diverging fungal lineages. Using single-molecule long-read sequencing of 16 diverse fungal genomes, we observed that up to 2.8% of all adenines were methylated in early-diverging fungi, far exceeding levels observed in other eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT dinucleotides and was concentrated in dense methylated adenine clusters surrounding the transcriptional start sites of expressed genes; its distribution was inversely correlated with that of 5-methylcytosine. Our results show a striking contrast in the genomic distributions of 6mA and 5-methylcytosine and reinforce a distinct role for 6mA as a gene-expression-associated epigenomic mark in eukaryotes.
Local amplifiers of IL-4Rα-mediated macrophage activation promote repair in lung and liver
May 12, 2017   Science (New York, N.Y.)
Minutti CM, Jackson-Jones LH, García-Fojeda B, Knipper JA, Sutherland TE,   . . . . . .   , Stamme C, Chroneos ZC, Zaiss DM, Casals C, Allen JE
Local amplifiers of IL-4Rα-mediated macrophage activation promote repair in lung and liver
May 12, 2017
Science (New York, N.Y.)
The type 2 immune response controls helminth infection and maintains tissue homeostasis but can lead to allergy and fibrosis if not adequately regulated. We have discovered local tissue-specific amplifiers of type-2 mediated-macrophage activation. In the lung, surfactant protein A (SP-A) enhanced IL-4-dependent macrophage proliferation and activation, accelerating parasite clearance and reducing pulmonary injury following infection with a lung-migrating helminth. In the peritoneal cavity and liver, C1q enhancement of type 2 macrophage activation was required for liver repair following bacterial infection, but resulted in fibrosis following peritoneal dialysis. IL-4 drives production of these structurally related defense collagens, SP-A and C1q, and the expression of their receptor, myosin 18A. These findings reveal the existence within different tissues of an amplification system needed for local type 2 responses. Copyright © 2017, American Association for the Advancement of Science.
Resistance to malaria through structural variation of red blood cell invasion receptors
May 19, 2017   Science (New York, N.Y.)
Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS,   . . . . . .   , Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP, Malaria Genomic Epidemiology Network
Resistance to malaria through structural variation of red blood cell invasion receptors
May 19, 2017
Science (New York, N.Y.)
The malaria parasite Plasmodium falciparum invades human red blood cells via interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy number variants affecting the host invasion receptor genes GYPA and GYPB We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently risen in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. Copyright © 2017, American Association for the Advancement of Science.
Ustilago maydis effectors and their impact on virulence
May 08, 2017   Nature Reviews. Microbiology
Lanver D, Tollot M, Schweizer G, Lo Presti L, Reissmann S, Ma LS, Schuster M, Tanaka S, Liang L, Ludwig N, Kahmann R
Ustilago maydis effectors and their impact on virulence
May 08, 2017
Nature Reviews. Microbiology
Biotrophic fungal plant pathogens establish an intimate relationship with their host to support the infection process. Central to this strategy is the secretion of a range of protein effectors that enable the pathogen to evade plant immune defences and modulate host metabolism to meet its needs. In this Review, using the smut fungus Ustilago maydis as an example, we discuss new insights into the effector repertoire of smut fungi that have been gained from comparative genomics and discuss the molecular mechanisms by which U. maydis effectors change processes in the plant host. Finally, we examine how the expression of effector genes and effector secretion are coordinated with fungal development in the host.
Mechanisms of gene flow in archaea
May 15, 2017   Nature Reviews. Microbiology
Wagner A, Whitaker RJ, Krause DJ, Heilers JH, van Wolferen M, van der Does C, Albers SV
Mechanisms of gene flow in archaea
May 15, 2017
Nature Reviews. Microbiology
Archaea are diverse, ecologically important, single-celled microorganisms. They have unique functions and features, such as methanogenesis and the composition of their cell envelope, although many characteristics are shared with the other domains of life, either through ancestry or through promiscuous horizontal gene transfer. The exchange of genetic material is a major driving force for genome evolution across the tree of life and has a role in archaeal speciation, adaptation and maintenance of diversity. In this Review, we discuss our current knowledge of archaeal mechanisms of DNA transfer and highlight the role of gene transfer in archaeal evolution.
Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation
May 20, 2017   Scientific Reports
Siles JA, Margesin R
Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation
May 20, 2017
Scientific Reports
The study of soil microbial responses to environmental changes is useful to improve simulation models and mitigation strategies for climate change. We here investigated two Alpine forest sites (deciduous forest vs. coniferous forest) situated at different altitudes (altitudinal effect) in spring and autumn (seasonal effect) regarding: (i) bacterial and fungal abundances (qPCR); (ii) diversity and structure of bacterial and fungal communities (amplicon sequencing); and (iii) diversity and composition of microbial functional gene community (Geochip 5.0). Significant altitudinal changes were detected in microbial abundances as well as in diversity and composition of taxonomic and functional communities as a consequence of the differences in pH, soil organic matter (SOM) and nutrient contents and soil temperatures measured between both sites. A network analysis revealed that deciduous forest site (at lower altitude) presented a lower resistance to environmental changes than that of coniferous forest site (at higher altitude). Significant seasonal effects were detected only for the diversity (higher values in autumn) and composition of microbial functional gene community, which was related to the non-significant increased SOM and nutrient contents detected in autumn respect to spring and the presumable high capacity of soil microbial communities to respond in functional terms to discreet environmental changes.

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