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1.
Braz J Med Biol Res ; 57: e13072, 2024.
Article in English | MEDLINE | ID: mdl-38451606

ABSTRACT

Immature hematopoietic progenitors are a constant source for renewal of hemocyte populations and the basic component of the tissue and cell repair apparatus. A unique property of these cells of internalizing extracellular double-stranded DNA has been previously shown. The leukostimulatory effect demonstrated in our pioneering studies was considered to be due to the feature of this cell. In the present research, we have analyzed the effects of DNA genome reconstructor preparation (DNAgr), DNAmix, and human recombinant angiogenin on both hematopoietic stem cells and multipotent progenitors. Treatment with bone marrow cells of experimental mice with these preparations stimulates colony formation by hematopoietic stem cells and proliferation of multipotent descendants. The main lineage responsible for this is the granulocyte-macrophage hematopoietic lineage. Using fluorescent microscopy as well as FACS assay, co-localization of primitive c-Kit- and Sca-1-positive progenitors and the TAMRA-labeled double-stranded DNA has been shown. Human recombinant angiogenin was used as a reference agent. Cells with specific markers were quantified in intact bone marrow and colonies grown in the presence of inducers. Quantitative analysis revealed that a total of 14,000 fragment copies of 500 bp, which is 0.2% of the haploid genome, can be delivered into early progenitors. Extracellular double-stranded DNA fragments stimulated the colony formation in early hematopoietic progenitors from the bone marrow, which assumed their effect on cells in G0. The observed number of Sca1+/c-Kit+ cells in colonies testifies to the possibility of both symmetrical and asymmetrical division of the initial hematopoietic stem cell and its progeny.


Subject(s)
Hematopoietic Stem Cells , Ribonuclease, Pancreatic , Humans , Animals , Mice , Ribonuclease, Pancreatic/pharmacology , Bone Marrow Cells , DNA
2.
Braz. j. med. biol. res ; 57: e13072, fev.2024. tab, graf
Article in English | LILACS-Express | LILACS | ID: biblio-1534067

ABSTRACT

Immature hematopoietic progenitors are a constant source for renewal of hemocyte populations and the basic component of the tissue and cell repair apparatus. A unique property of these cells of internalizing extracellular double-stranded DNA has been previously shown. The leukostimulatory effect demonstrated in our pioneering studies was considered to be due to the feature of this cell. In the present research, we have analyzed the effects of DNA genome reconstructor preparation (DNAgr), DNAmix, and human recombinant angiogenin on both hematopoietic stem cells and multipotent progenitors. Treatment with bone marrow cells of experimental mice with these preparations stimulates colony formation by hematopoietic stem cells and proliferation of multipotent descendants. The main lineage responsible for this is the granulocyte-macrophage hematopoietic lineage. Using fluorescent microscopy as well as FACS assay, co-localization of primitive c-Kit- and Sca-1-positive progenitors and the TAMRA-labeled double-stranded DNA has been shown. Human recombinant angiogenin was used as a reference agent. Cells with specific markers were quantified in intact bone marrow and colonies grown in the presence of inducers. Quantitative analysis revealed that a total of 14,000 fragment copies of 500 bp, which is 0.2% of the haploid genome, can be delivered into early progenitors. Extracellular double-stranded DNA fragments stimulated the colony formation in early hematopoietic progenitors from the bone marrow, which assumed their effect on cells in G0. The observed number of Sca1+/c-Kit+ cells in colonies testifies to the possibility of both symmetrical and asymmetrical division of the initial hematopoietic stem cell and its progeny.

3.
J Synchrotron Radiat ; 29(Pt 3): 595-601, 2022 May 01.
Article in English | MEDLINE | ID: mdl-35510992

ABSTRACT

X-ray free-electron lasers (XFELs) deliver pulses of coherent X-rays on the femtosecond time scale, with potentially high repetition rates. While XFELs provide high peak intensities, both the intensity and the centroid of the beam fluctuate strongly on a pulse-to-pulse basis, motivating high-rate beam diagnostics that operate over a large dynamic range. The fast drift velocity, low X-ray absorption and high radiation tolerance properties of chemical vapour deposition diamonds make these crystals a promising candidate material for developing a fast (multi-GHz) pass-through diagnostic for the next generation of XFELs. A new approach to the design of a diamond sensor signal path is presented, along with associated characterization studies performed in the XPP endstation of the LINAC Coherent Light Source (LCLS) at SLAC. Qualitative charge collection profiles (collected charge versus time) are presented and compared with those from a commercially available detector. Quantitative results on the charge collection efficiency and signal collection times are presented over a range of approximately four orders of magnitude in the generated electron-hole plasma density.

4.
Sci Immunol ; : eabo0535, 2022 03 10.
Article in English | MEDLINE | ID: mdl-35271298

ABSTRACT

SARS-CoV-2 primarily replicates in mucosal sites, and more information is needed about immune responses in infected tissues. Here, we used rhesus macaques to model protective primary immune responses in tissues during mild COVID-19. Viral RNA levels were highest on days 1-2 post-infection and fell precipitously thereafter. 18F-fluorodeoxyglucose (FDG)-avid lung abnormalities and interferon (IFN)-activated monocytes and macrophages in the bronchoalveolar lavage (BAL) were found on days 3-4 post-infection. Virus-specific effector CD8+ and CD4+ T cells became detectable in the BAL and lung tissue on days 7-10, after viral RNA, radiologic evidence of lung inflammation, and IFN-activated myeloid cells had substantially declined. Notably, SARS-CoV-2-specific T cells were not detectable in the nasal turbinates, salivary glands, and tonsils on day 10 post-infection. Thus, SARS-CoV-2 replication wanes in the lungs of rhesus macaques prior to T cell responses, and in the nasal and oral mucosa despite the apparent lack of antigen-specific T cells, suggesting that innate immunity efficiently restricts viral replication during mild COVID-19.

5.
J Immunother Cancer ; 9(11)2021 11.
Article in English | MEDLINE | ID: mdl-34799399

ABSTRACT

BACKGROUND: NIZ985 is a recombinant heterodimer of physiologically active interleukin (IL-)15 and IL-15 receptor alpha. In preclinical models, NIZ985 promotes cytotoxic lymphocyte proliferation, killing function, and organ/tumor infiltration, with resultant anticancer effects. In this first-in-human study, we assessed the safety, pharmacokinetics, and immune effects of NIZ985 in patients with metastatic or unresectable solid tumors. METHODS: Single agent NIZ985 dose escalation data are reported from a phase I dose escalation/expansion study of NIZ985 as monotherapy. Adult patients (N=14) received 0.25, 0.5, 1, 2 or 4 µg/kg subcutaneous NIZ985 three times weekly (TIW) for the first 2 weeks of each 28-day cycle, in an accelerated 3+3 dose escalation trial design. IL-15 and endogenous cytokines were monitored by ELISA and multiplexed electrochemiluminescent assays. Multiparameter flow cytometry assessed the frequency, phenotype and proliferation of peripheral blood mononuclear cells. Preliminary antitumor activity was assessed by overall response rate (Response Evaluation Criteria in Solid Tumors V.1.1). RESULTS: As of March 2, 2020, median treatment duration was 7.5 weeks (range 1.1-77.1). Thirteen patients had discontinued and one (uveal melanoma) remains on treatment with stable disease. Best clinical response was stable disease (3 of 14 patients; 21%). The most frequent adverse events (AEs) were circular erythematous injection site reactions (100%), chills (71%), fatigue (57%), and fever (50%). Treatment-related grade 3/4 AEs occurred in six participants (43%); treatment-related serious AEs (SAEs) in three (21%). The per-protocol maximum tolerated dose was not reached. Pharmacokinetic accumulation of serum IL-15 in the first week was followed by significantly lower levels in week 2, likely due to more rapid cytokine consumption by an expanding lymphocyte pool. NIZ985 treatment was associated with increases in several cytokines, including interferon (IFN)-γ, IL-18, C-X-C motif chemokine ligand 10, and tumor necrosis factor-ß, plus significant induction of cytotoxic lymphocyte proliferation (including natural killer and CD8+ T cells), increased CD16+ monocytes, and increased CD163+ macrophages at injection sites. CONCLUSIONS: Subcutaneous NIZ985 TIW was generally well tolerated in patients with advanced cancer and produced immune activation paralleling preclinical observations, with induction of IFN-γ and proliferation of cytotoxic lymphocytes. Due to delayed SAEs at the two highest dose levels, administration is being changed to once-weekly in a revised protocol, as monotherapy and combined with checkpoint inhibitor spartalizumab. These alterations are expected to maximize the potential of NIZ985 as a novel immunotherapy. TRIAL REGISTRATION NUMBER: NCT02452268.


Subject(s)
Interleukin-15/administration & dosage , Interleukin-15/agonists , Neoplasms/drug therapy , Receptors, Interleukin-15/administration & dosage , Adult , Aged , Female , Humans , Immunotherapy , Male , Middle Aged , Neoplasm Metastasis , Protein Multimerization , Recombinant Proteins/administration & dosage
6.
J Hosp Infect ; 112: 104-107, 2021 Jun.
Article in English | MEDLINE | ID: mdl-33864893

ABSTRACT

Personal protective equipment (PPE) is essential for healthcare worker (HCW) safety. Conservation of PPE for clinical use during the COVID-19 pandemic reduced its availability for training, necessitating an innovative approach to sourcing high physical resemblance PPE (HPR-PPE). We present a case study of crowd-sourcing of HPR-PPE to train HCWs. Survey results indicated that HPR-PPE enabled high-fidelity practise of PPE application and removal, aided procedure recall, improved user confidence and was sufficiently similar to medical-grade PPE. HPR-PPE provided a novel and cost-effective alternative. We also demonstrated that medical-grade PPE can be sourced from non-medical institutions and businesses during a pandemic.


Subject(s)
COVID-19/prevention & control , Health Personnel/education , Infection Control/methods , Infectious Disease Transmission, Patient-to-Professional/prevention & control , Personal Protective Equipment/supply & distribution , Case-Control Studies , Crowdsourcing , Durable Medical Equipment , Humans , Infection Control/instrumentation , Qualitative Research , Respiratory Protective Devices , Simulation Training
7.
Sci Transl Med ; 13(576)2021 01 13.
Article in English | MEDLINE | ID: mdl-33441422

ABSTRACT

Organ infiltration by donor T cells is critical to the development of acute graft-versus-host disease (aGVHD) in recipients after allogeneic hematopoietic stem cell transplant (allo-HCT). However, deconvoluting the transcriptional programs of newly recruited donor T cells from those of tissue-resident T cells in aGVHD target organs remains a challenge. Here, we combined the serial intravascular staining technique with single-cell RNA sequencing to dissect the tightly connected processes by which donor T cells initially infiltrate tissues and then establish a pathogenic tissue residency program in a rhesus macaque allo-HCT model that develops aGVHD. Our results enabled creation of a spatiotemporal map of the transcriptional programs controlling donor CD8+ T cell infiltration into the primary aGVHD target organ, the gastrointestinal (GI) tract. We identified the large and small intestines as the only two sites demonstrating allo-specific, rather than lymphodepletion-driven, T cell infiltration. GI-infiltrating donor CD8+ T cells demonstrated a highly activated, cytotoxic phenotype while simultaneously developing a canonical tissue-resident memory T cell (TRM) transcriptional signature driven by interleukin-15 (IL-15)/IL-21 signaling. We found expression of a cluster of genes directly associated with tissue invasiveness, including those encoding adhesion molecules (ITGB2), specific chemokines (CCL3 and CCL4L1) and chemokine receptors (CD74), as well as multiple cytoskeletal proteins. This tissue invasion transcriptional signature was validated by its ability to discriminate the CD8+ T cell transcriptome of patients with GI aGVHD from those of GVHD-free patients. These results provide insights into the mechanisms controlling tissue occupancy of target organs by pathogenic donor CD8+ TRM cells during aGVHD in primate transplant recipients.


Subject(s)
Graft vs Host Disease , Hematopoietic Stem Cell Transplantation , Acute Disease , Animals , CD8-Positive T-Lymphocytes , Humans , Macaca mulatta , Tissue Donors
8.
Sci Transl Med ; 13(576)2021 01 13.
Article in English | MEDLINE | ID: mdl-33441427

ABSTRACT

Leukocyte trafficking enables detection of pathogens, immune responses, and immune memory. Dysregulation of leukocyte trafficking is often found in disease, highlighting its important role in homeostasis and the immune response. Whereas some of the molecular mechanisms mediating leukocyte trafficking are understood, little is known about the regulation of trafficking, including trafficking kinetics and its impact on immune homeostasis. We developed a method of serial intravascular staining (SIVS) to measure trafficking kinetics in nonhuman primates using infusions of fluorescently labeled antibodies to label circulating leukocytes. Because antibody infusions labeled only leukocytes in the blood, cells were "barcoded" according to their location at the time of each infusion, providing positional histories that could be used to infer trafficking kinetics. We used SIVS and multiparameter flow cytometry to quantitate cellular trafficking into lymphoid tissues of healthy animals at homeostasis and to identify perivascular cells that could be unique to nonlymphoid organs. To investigate how these parameters could be influenced during disease, SIVS was used to quantify lymphocyte trafficking in macaques infected with the bacterial pathogen Mycobacterium tuberculosis and to enumerate intravascular leukocytes in lung granulomas. We showed that whereas most cells in lung granulomas were localized there for more than 24 hours, granulomas were dynamic with a slow continual cellular influx, the rate of which predicted clearance of M. tuberculosis from the granulomas. SIVS, in combination with intracellular staining and multiparametric flow cytometry, is a powerful method to quantify the kinetics of leukocyte trafficking in nonhuman primates in vivo.


Subject(s)
Mycobacterium tuberculosis , Animals , Kinetics , Leukocytes , Lymphoid Tissue , Staining and Labeling
9.
Front Immunol ; 12: 772332, 2021.
Article in English | MEDLINE | ID: mdl-35095846

ABSTRACT

The in vivo tissue distribution and trafficking patterns of natural killer (NK) cells remain understudied. Animal models can help bridge the gap, and rhesus macaque (RM) primates faithfully recapitulate key elements of human NK cell biology. Here, we profiled the tissue distribution and localization patterns of three NK cell subsets across various RM tissues. We utilized serial intravascular staining (SIVS) to investigate the tissue trafficking kinetics at steady state and during recovery from CD16 depletion. We found that at steady state, CD16+ NK cells were selectively retained in the vasculature while CD56+ NK cells had a shorter residence time in peripheral blood. We also found that different subsets of NK cells had distinct trafficking kinetics to and from the lymph node as well as other lymphoid and non-lymphoid tissues. Lastly, we found that following administration of CD16-depleting antibody, CD16+ NK cells and their putative precursors retained a high proportion of continuously circulating cells, suggesting that regeneration of the CD16 NK compartment may take place in peripheral blood or the perivascular compartments of tissues.


Subject(s)
Killer Cells, Natural/immunology , Macaca mulatta/immunology , Animals , CD56 Antigen/immunology , Kinetics , Lymph Nodes/immunology , Staining and Labeling
10.
Vavilovskii Zhurnal Genet Selektsii ; 24(6): 643-652, 2020 Oct.
Article in Russian | MEDLINE | ID: mdl-33659850

ABSTRACT

The paper describes some biological features of the radioprotective effect of double-stranded RNA preparation. It was found that yeast RNA preparation has a prolonged radioprotective effect after irradiation by a lethal dose of 9.4 Gy. 100 % of animals survive on the 70th day of observation when irradiated 1 hour or 4 days after 7 mg RNA preparation injection, 60 % animals survive when irradiated on day 8 or 12. Time parameters of repair of double-stranded breaks induced by gamma rays were estimated. It was found that the injection of the RNA preparation at the time of maximum number of double-stranded breaks, 1 hour after irradiation, reduces the efficacy of radioprotective action compared with the injection 1 hour before irradiation and 4 hours after irradiation. A comparison of the radioprotective effect of the standard radioprotector B-190 and the RNA preparation was made in one experiment. It has been established that the total RNA preparation is more efficacious than B-190. Survival on the 40th day after irradiation was 78 % for the group of mice treated with the RNA preparation and 67 % for those treated with B-190. In the course of analytical studies of the total yeast RNA preparation, it was found that the preparation is a mixture of single-stranded and double-stranded RNA. It was shown that only double-stranded RNA has radioprotective properties. Injection of 160 µg double-stranded RNA protects 100 % of the experimental animals from an absolutely lethal dose of gamma radiation, 9.4 Gy. It was established that the radioprotective effect of double-stranded RNA does not depend on sequence, but depends on its double-stranded form and the presence of "open" ends of the molecule. It is supposed that the radioprotective effect of double-stranded RNA is associated with the participation of RNA molecules in the correct repair of radiation-damaged chromatin in blood stem cells. The hematopoietic pluripotent cells that have survived migrate to the periphery, reach the spleen and actively proliferate. The newly formed cell population restores the hematopoietic and immune systems, which determines the survival of lethally irradiated animals.

11.
Clin Cancer Res ; 25(16): 4945-4954, 2019 08 15.
Article in English | MEDLINE | ID: mdl-31142503

ABSTRACT

PURPOSE: The first-in-human clinical trial with human bolus intravenous infusion IL15 (rhIL15) was limited by treatment-associated toxicity. Here, we report toxicity, immunomodulation, and clinical activity of rhIL15 administered as a 10-day continuous intravenous infusion (CIV) to patients with cancers in a phase I trial. PATIENTS AND METHODS: Patients received treatment for 10 days with CIV rhIL15 in doses of 0.125, 0.25, 0.5, 1, 2, or 4 µg/kg/day. Correlative laboratory tests included IL15 pharmacokinetic (PK) analyses, and assessment of changes in lymphocyte subset numbers. RESULTS: Twenty-seven patients were treated with rhIL15; 2 µg/kg/day was identified as the MTD. There were eight serious adverse events including two bleeding events, papilledema, uveitis, pneumonitis, duodenal erosions, and two deaths (one due to likely drug-related gastrointestinal ischemia). Evidence of antitumor effects was observed in several patients, but stable disease was the best response noted. Patients in the 2 µg/kg/day group had a 5.8-fold increase in number of circulating CD8+ T cells, 38-fold increase in total NK cells, and 358-fold increase in CD56bright NK cells. Serum IL15 concentrations were markedly lower during the last 3 days of infusion. CONCLUSIONS: This phase I trial identified the MTD for CIV rhIL15 and defined a treatment regimen that produced significant expansions of CD8+ T and NK effector cells in circulation and tumor deposits. This regimen has identified several biological features, including dramatic increases in numbers of NK cells, supporting trials of IL15 with anticancer mAbs to increase antibody-dependent cell-mediated cytotoxicity and anticancer efficacy.


Subject(s)
Interleukin-15/administration & dosage , Killer Cells, Natural/drug effects , Killer Cells, Natural/immunology , Lymphocyte Subsets/drug effects , Lymphocyte Subsets/immunology , Neoplasms/drug therapy , Neoplasms/immunology , Cytokines/metabolism , Female , Humans , Immunohistochemistry , Immunologic Factors/administration & dosage , Immunologic Factors/adverse effects , Immunologic Factors/pharmacokinetics , Immunomodulation/drug effects , Inflammation Mediators/metabolism , Infusions, Intravenous , Interleukin-15/adverse effects , Interleukin-15/pharmacokinetics , Killer Cells, Natural/metabolism , Lymphocyte Activation/drug effects , Lymphocyte Activation/immunology , Lymphocyte Count , Lymphocyte Subsets/metabolism , Lymphocytes, Tumor-Infiltrating/drug effects , Lymphocytes, Tumor-Infiltrating/immunology , Lymphocytes, Tumor-Infiltrating/metabolism , Neoplasms/diagnosis , Neoplasms/metabolism , Treatment Outcome
12.
Nat Commun ; 10(1): 948, 2019 02 27.
Article in English | MEDLINE | ID: mdl-30814513

ABSTRACT

An array of carbohydrates masks the HIV-1 surface protein Env, contributing to the evasion of humoral immunity. In most HIV-1 isolates 'glycan holes' occur due to natural sequence variation, potentially revealing the underlying protein surface to the immune system. Here we computationally design epitopes that mimic such surface features (carbohydrate-occluded neutralization epitopes or CONE) of Env through 'epitope transplantation', in which the target region is presented on a carrier protein scaffold with preserved structural properties. Scaffolds displaying the four CONEs are examined for structure and immunogenicity. Crystal structures of two designed proteins reflect the computational models and accurately mimic the native conformations of CONEs. The sera from rabbits immunized with several CONE immunogens display Env binding activity. Our method determines essential structural elements for targets of protective antibodies. The ability to design immunogens with high mimicry to viral proteins also makes possible the exploration of new templates for vaccine development.


Subject(s)
AIDS Vaccines/immunology , HIV Antibodies/biosynthesis , HIV Antibodies/immunology , HIV-1/immunology , env Gene Products, Human Immunodeficiency Virus/immunology , Amino Acid Sequence , Animals , Antibodies, Neutralizing/biosynthesis , Antibodies, Neutralizing/immunology , Biophysical Phenomena , Carbohydrates/chemistry , Carbohydrates/immunology , Crystallography, X-Ray , Epitopes/chemistry , Epitopes/genetics , Epitopes/immunology , HIV Antigens/chemistry , HIV Antigens/genetics , HIV Antigens/immunology , Humans , Models, Molecular , Protein Conformation , Protein Engineering , Rabbits , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/immunology , env Gene Products, Human Immunodeficiency Virus/chemistry , env Gene Products, Human Immunodeficiency Virus/genetics
13.
J Exp Med ; 215(1): 217-232, 2018 01 02.
Article in English | MEDLINE | ID: mdl-29141868

ABSTRACT

The geographic distribution of hematopoiesis at a clonal level is of interest in understanding how hematopoietic stem and progenitor cells (HSPCs) and their progeny interact with bone marrow (BM) niches during regeneration. We tagged rhesus macaque autologous HSPCs with genetic barcodes, allowing clonal tracking over time and space after transplantation. We found marked geographic segregation of CD34+ HSPCs for at least 6 mo posttransplantation, followed by very gradual clonal mixing at different BM sites over subsequent months to years. Clonal mapping was used to document local production of granulocytes, monocytes, B cells, and CD56+ natural killer (NK) cells. In contrast, CD16+CD56- NK cells were not produced in the BM, and in fact were clonally distinct from multipotent progenitors producing all other lineages. Most surprisingly, we documented local BM production of CD3+ T cells early after transplantation, using both clonal mapping and intravascular versus tissue-resident T cell staining, suggesting a thymus-independent T cell developmental pathway operating during BM regeneration, perhaps before thymic recovery.


Subject(s)
Cell Differentiation , Cell Movement , Cell Tracking , Clonal Evolution , Hematopoiesis , Hematopoietic Stem Cells/cytology , Hematopoietic Stem Cells/metabolism , Animals , Biomarkers , Bone Marrow , Bone Marrow Cells/cytology , Bone Marrow Cells/metabolism , Cell Lineage , Cell Tracking/methods , Cellular Microenvironment , Hematopoietic Stem Cell Transplantation , Immunophenotyping , Lymph Nodes/cytology , Lymph Nodes/metabolism , Macaca mulatta , Time Factors
15.
Article in English | MEDLINE | ID: mdl-24215551

ABSTRACT

Foods may be irradiated in their final packaging and this process may affect the composition of the packaging and in turn affect the migration of substances into food. Headspace and liquid injection GC-MS and HPLC with time-of-flight MS have been used to identify and estimate levels of radiolytic products in irradiated finished plastic packaging materials. Fifteen retail packaging materials were studied. Investigations were carried out into the effect of different irradiation types (gamma and electron beam), irradiation doses (1, 3, 7 and 10 kGy) and dose rates (5 kGy s(-1) for electron beam and 0.4 and 1.85 kGy h(-1) for gamma) on the radiolytic products. Any differences seen in comparing the two ionising radiation types were attributed largely to the very different dose rates; for electron beam a 10 kGy dose was delivered in just 2 s whereas using gamma it took 5.4 h. Differences were also seen when comparing the same samples irradiated at different doses. Some substances were not affected by irradiation, others decreased in concentration and others were formed upon increasing doses of irradiation. These results confirm that irradiation-induced changes do occur in substances with the potential to migrate and that the safety of the finished packaging material following irradiation should be assessed.


Subject(s)
Food Contamination/analysis , Food Irradiation/adverse effects , Food Packaging , Chromatography, High Pressure Liquid , Coloring Agents/radiation effects , Dose-Response Relationship, Radiation , Electrons/adverse effects , Gamma Rays/adverse effects , Gas Chromatography-Mass Spectrometry , Hazard Analysis and Critical Control Points/methods , Humans , Ink , Spectrometry, Mass, Electrospray Ionization
16.
J Virol ; 87(13): 7218-33, 2013 Jul.
Article in English | MEDLINE | ID: mdl-23616655

ABSTRACT

Understanding human immunodeficiency virus type 1 (HIV-1) transmission is central to developing effective prevention strategies, including a vaccine. We compared phenotypic and genetic variation in HIV-1 env genes from subjects in acute/early infection and subjects with chronic infections in the context of subtype C heterosexual transmission. We found that the transmitted viruses all used CCR5 and required high levels of CD4 to infect target cells, suggesting selection for replication in T cells and not macrophages after transmission. In addition, the transmitted viruses were more likely to use a maraviroc-sensitive conformation of CCR5, perhaps identifying a feature of the target T cell. We confirmed an earlier observation that the transmitted viruses were, on average, modestly underglycosylated relative to the viruses from chronically infected subjects. This difference was most pronounced in comparing the viruses in acutely infected men to those in chronically infected women. These features of the transmitted virus point to selective pressures during the transmission event. We did not observe a consistent difference either in heterologous neutralization sensitivity or in sensitivity to soluble CD4 between the two groups, suggesting similar conformations between viruses from acute and chronic infection. However, the presence or absence of glycosylation sites had differential effects on neutralization sensitivity for different antibodies. We suggest that the occasional absence of glycosylation sites encoded in the conserved regions of env, further reduced in transmitted viruses, could expose specific surface structures on the protein as antibody targets.


Subject(s)
Genetic Variation , HIV Infections/metabolism , HIV-1/metabolism , Receptors, CCR5/metabolism , T-Lymphocytes/virology , Viral Envelope Proteins/metabolism , Base Sequence , Cloning, Molecular , Cluster Analysis , Cohort Studies , Female , Glycosylation , HIV Infections/prevention & control , HIV Infections/transmission , Humans , Malawi , Male , Molecular Sequence Data , Neutralization Tests , Phylogeny , Protein Conformation , Receptors, CCR5/chemistry , Sequence Alignment , Sequence Analysis, DNA , Sex Factors , South Africa , T-Lymphocytes/immunology , Viral Envelope Proteins/genetics , Virus Replication/physiology
17.
PLoS Pathog ; 9(4): e1003294, 2013.
Article in English | MEDLINE | ID: mdl-23593004

ABSTRACT

RNA secondary structure plays a central role in the replication and metabolism of all RNA viruses, including retroviruses like HIV-1. However, structures with known function represent only a fraction of the secondary structure reported for HIV-1(NL4-3). One tool to assess the importance of RNA structures is to examine their conservation over evolutionary time. To this end, we used SHAPE to model the secondary structure of a second primate lentiviral genome, SIVmac239, which shares only 50% sequence identity at the nucleotide level with HIV-1NL4-3. Only about half of the paired nucleotides are paired in both genomic RNAs and, across the genome, just 71 base pairs form with the same pairing partner in both genomes. On average the RNA secondary structure is thus evolving at a much faster rate than the sequence. Structure at the Gag-Pro-Pol frameshift site is maintained but in a significantly altered form, while the impact of selection for maintaining a protein binding interaction can be seen in the conservation of pairing partners in the small RRE stems where Rev binds. Structures that are conserved between SIVmac239 and HIV-1(NL4-3) also occur at the 5' polyadenylation sequence, in the plus strand primer sites, PPT and cPPT, and in the stem-loop structure that includes the first splice acceptor site. The two genomes are adenosine-rich and cytidine-poor. The structured regions are enriched in guanosines, while unpaired regions are enriched in adenosines, and functionaly important structures have stronger base pairing than nonconserved structures. We conclude that much of the secondary structure is the result of fortuitous pairing in a metastable state that reforms during sequence evolution. However, secondary structure elements with important function are stabilized by higher guanosine content that allows regions of structure to persist as sequence evolution proceeds, and, within the confines of selective pressure, allows structures to evolve.


Subject(s)
Genome, Viral , HIV-1/genetics , Nucleic Acid Conformation , RNA, Viral/chemistry , RNA, Viral/genetics , Simian Immunodeficiency Virus/genetics , Animals , Base Composition , Base Sequence , Binding Sites , Evolution, Molecular , Frameshift Mutation , Genes, env/genetics , Humans , Mice , RNA-Binding Proteins/metabolism , Sequence Alignment , Sequence Homology, Nucleic Acid
18.
Sci Total Environ ; 431: 252-61, 2012 Aug 01.
Article in English | MEDLINE | ID: mdl-22687435

ABSTRACT

Estimates of absorbed dose rates to wildlife from exposure to natural background radionuclides are required to put estimates of dose rates arising from regulated releases of radioactivity and proposed benchmarks into context. Recent review papers have estimated dose rates to wildlife from (40)K, and (238)U and (232)Th series radionuclides. However, only one study previous has considered the potential dose rates to burrowing animals from inhaled (222)Rn and its daughter products. In this paper we describe a study conducted at seven sites in northwest England. Passive track etch detectors were used to measure the (222)Rn concentrations in artificial burrows over a period of approximately one year. Results suggest that absorbed dose rates to burrowing mammals as a consequence of exposure to (222)Rn are likely to be at least an order of magnitude higher than those suggested in previous evaluations of natural background exposure rates which had omitted this radionuclide and exposure pathway. Dose rates in some areas of Great Britain will be considerably in excess of incremental no-effects benchmark dose rates suggested for use as screening levels. Such advised benchmark dose rates need to be better put into context with background dose rates, including exposure to (222)Rn, to ensure credibility; although the context will be determined by the purpose of the benchmark and the assessment level.


Subject(s)
Environmental Exposure , Mammals , Radon/analysis , Radon/toxicity , Animals , Behavior, Animal , England , Mammals/physiology , Radiometry/instrumentation , Radiometry/methods , Temperature , Whole-Body Irradiation
20.
Article in English | MEDLINE | ID: mdl-20486003

ABSTRACT

Fifty melamine-ware articles were tested for the migration of formaldehyde - with hexamethylenetetramine (HMTA) expressed as formaldehyde - to see whether the total specific migration limit (SML(T)) was being observed. The SML(T), given in European Commission Directive 2002/72/EC as amended, is 15 mg kg(-1). Fourier transform-infrared (FT-IR) spectroscopy was carried out on the articles to confirm the plastic type. Articles were exposed to the food simulant 3% (w/v) aqueous acetic acid under conditions representing their worst foreseeable use. Formaldehyde and HMTA in food simulants were determined by a spectrophotometric derivatization procedure. Positive samples were confirmed by a second spectrophotometric procedure using an alternative derivatization agent. As all products purchased were intended for repeat use, three sequential exposures to the simulant were carried out. Formaldehyde was detected in the simulant exposed to 43 samples. Most of the levels found were well below the limits set in law such that 84% of the samples tested were compliant. However, eight samples had formaldehyde levels that were clearly above the legal maximum at six to 65 times the SML(T).


Subject(s)
Food Contamination/analysis , Formaldehyde/chemistry , Plastics/chemistry , Color , Cooking and Eating Utensils/standards , Equipment Design , United Kingdom
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