Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw accuracy of the aligned reads to >99.9%, allowing us to accurately call SNPs with as few as two reads per allele. We collected several billion mate-paired reads yielding approximately 18x haploid coverage of aligned sequence and close to 300x clone coverage. Over 98% of the reference genome is covered with at least one uniquely placed read, and 99.65% is spanned by at least one uniquely placed mate-paired clone. We identify over 3.8 million SNPs, 19% of which are novel. Mate-paired data are used to physically resolve haplotype phases of nearly two-thirds of the genotypes obtained and produce phased segments of up to 215 kb. We detect 226,529 intra-read indels, 5590 indels between mate-paired reads, 91 inversions, and four gene fusions. We use a novel approach for detecting indels between mate-paired reads that are smaller than the standard deviation of the insert size of the library and discover deletions in common with those detected with our intra-read approach. Dozens of mutations previously described in OMIM and hundreds of nonsynonymous single-nucleotide and structural variants in genes previously implicated in disease are identified in this individual. There is more genetic variation in the human genome still to be uncovered, and we provide guidance for future surveys in populations and cancer biopsies.

Abnormal bronchoalveolar lavage in asymptomatic dairy farmers. Study of lymphocytes

Bronchoalveolar lavage (BAL) was performed on 24 asymptomatic dairy farmers. Thirteen had serum precipitins to Micropolyspora faeni (MF) antigens (Group 1), and 11 were seronegative control subjects (Group 2). All were nonsmokers and had no history of previous lung disease. Thirteen of 24 subjects (9 in Group 1 and 4 in Group 2) had a high percentage of lymphocytes (greater than or equal to 20%) in their BAL. The T-lymphocyte subpopulations as estimated by OKT3, OKT4, and OKT8 monoclonal antibody reactivity were measured in peripheral blood lymphocytes; OKT3 = 58.5 +/- 15.6% for Group 1, and 58.5 +/- 8.7% for Group 2; OKT4 = 40.6 +/- 10.7% and 39.9 +/- 10.0%; OKT8 = 21.5 +/- 10.6% and 22.4 +/- 8.0%, respectively (p = NS). These lymphocyte characteristics were also similar when subjects with a high percentage of lymphocytes in BAL were compared to those with a normal percentage. Specific (MF-coated) chicken erythrocyte lymphocytotoxicity (Group 1, 45.2 +/- 29.5%, Group 2, 49.2 +/- 23.4%), and nonspecific lymphocytotoxicity (Group 1, 43.9 +/- 28.6%, Group 2, 37.9 +/- 18.0%) were also similar. We conclude that a large number of asymptomatic dairy farmers have an increased percentage of lymphocytes in their BAL ("alveolitis") and that peripheral blood lymphocytes in these subjects have normal subpopulations, as assessed by monoclonal antibodies, and normal lymphocytotoxicity.

Improved renal allograft function and survival following nonspecific blood transfusions. I. Induction of soluble suppressor factors inhibiting the mitogenic response

A small number of blood transfusions (1-3) seems sufficient to improve the cadaveric renal allograft outcome, probably via induction of some nonspecific suppressive activity. This activity was assessed by the concanavalin A (Con A) enhancement method; when present, the response of freshly isolated patients' cells to a submitogenic dose of Con A was lowered, leading to a Con A ratio greater than 5, significantly (P less than 0.0001) higher than the one observed in normal controls or untransfused uremic patients. The correlation between this suppressive activity and graft outcome was determined. Thirty-five patients were studied over a 12-month period for graft function (creatinine level) and survival. Both parameters were significantly improved in the group of patients whose Con A ratio was greater than 5 after transfusions. A soluble suppressor factor, or factors, released into the supernatant of patients' lymphocytes cultured for 48 hr, seems responsible for this suppressive activity. Moreover this process is nonspecific, since it suppresses mitogenic response of cells isolated from normal untransfused volunteers, and could be observed when peripheral blood mononuclear cells were used, but not with purified adherent or nonadherent cells. Addition of indomethacin to the cells during the elaboration of the supernatant abolished this activity. However, amounts of PGE2 secreted into the supernatant during the 48 hr of culture could not be correlated with this suppressive activity. These findings suggest that induction of nonspecific immunosuppression by a few blood transfusions could predict a better kidney graft outcome.

Transformation/dissolution examination of antimony and antimony compounds with speciation of the transformation/dissolution solutions

Speciation is held to be a key factor in controlling the ecotoxicity of metals in solution. Using the United Nations transformation/dissolution protocol (T/DP) for metals and sparingly soluble metal compounds, we have examined the transformation/dissolution (T/D) characteristics in terms of the concentrations of total dissolved Sb at pH 6 and 8.5 in 1, 10, and 100 mg/L loadings over 7 d as well as the concentrations of Sb(III) and Sb(V) at the 1 mg/L loadings over 28 d, of sodium hexahydroxoantimonate (NaSb(OH)(6)), antimony metal (Sb), antimony trioxide (Sb(2) O(3)), antimony sulfide (Sb(2) S(3)), sodium antimonate (NaSbO(3)), antimony tris(ethylene glycolate) (Sb(2) (C(2) H(4) O(2) )(3)), antimony trichloride (SbCl(3)), antimony triacetate (Sb(CH(3) COO)(3)), and antimony pentoxide (Sb(2) O(5) ). We also measured the concentrations of the dissolved Sb(III) and Sb(V) species at the 1 mg/L loadings. Because of complexing, the trivalent organic Sb compounds exhibited little or no oxidation of Sb(III) to Sb(V). However, oxidation of Sb(III) to Sb(V) was evident for the trivalent inorganic Sb compounds. Conversely, with pentavalent Sb compounds, there was no reduction of Sb(V) to Sb(III). Based on the percentage of Sb in the compound dissolved or metal reacted at 28 d and 1 mg/L loadings, the solubility rankings at pH 6 are NaSb(OH)(6)  > Sb(CH(3) COO)(3)  > Sb metal > Sb(2) (C(2) H(4) O(2))(3)  > Sb(2) S(3)  > Sb(2) O(3)  > NaSbO(3)  ≈ SbCl(3)  > Sb(2) O(5). For pH 8.5 the order is NaSb(OH)(6)  > Sb(CH(3) COO)(3)  > Sb metal > Sb(2) (C(2) H(4) O(2) )(3)  > SbCl(3)  > Sb(2) O(3)  > Sb(2) S(3)  > NaSbO(3)  > Sb(2) O(5) . We provide worked examples of how the T/D data have been used to derive hazard classification proposals for Sb metal and these selected compounds for submission to the European Chemicals Agency under the Registration, Evaluation, Authorization and Restriction of CHemicals (REACH) legislation.

Method Development for Determining the Removal of Metals from the Water Column under Transformation/Dissolution Conditions for Chronic Hazard Classification

An extension of the transformation/dissolution protocol (T/DP) was developed and evaluated as a tool to measure the removal of metals from the water column for chronic aquatic hazard classification. The T/DP extension (T/DP-E) consists of 2 parts: T/DP-E part 1, to measure metal removal from the water column via binding of metals to a substrate and subsequent settling, and T/DP-E part 2, to assess the potential for remobilization of metals following resuspension. The T/DP-E methodology (672-h [28-d] removal period, 1-h resuspension event, and 96-h resettling period) was tested using Cu, Co, and Sr solutions in the presence of a substrate. The metal removal rates varied from rapid removal for Cu to slower rates of removal for Co and Sr. The resuspension event did not trigger any increase in dissolved Cu, Co, or Sr. Additional 96-h experiments were conducted using dissolved Ni, Pb, Zn, and Ag and supported the conclusion that the T/DP-E is sufficiently robust to distinguish removal rates between metals with a wide range of reactivities. The proposed method provides a means to quantify the rate of metal removal from the water column and evaluate remobilization potential in a standardized and reliable way. Environ Toxicol Chem 2019;38:2032-2042. © 2019 SETAC.

Detection of immunoglobulin-secreting lymphocytes by the use of a hemolytic plaque assay in liquid phase

This paper describes a modification of the reverse hemolytic plaque assay allowing the enumeration of immunoglobulin (Ig)-secreting lymphocytes at rest or after in vitro stimulation. Ig-secreting cells are mixed with anti-Ig coated sheep red blood cells, developing anti-Ig antiserum and complement in liquid medium. This mixture is pipetted between two slides and the hemolytic plaques are numerated after incubation at 37 degrees C. The class of Ig secreted can be determined using a monospecific developing antiserum. This technique is easier to perform and more economical than the previously described method using agarose without loss of sensitivity, the number of plaques detected being about the same and the kinetic of their appearance comparable.

Blood transfusions in renal dialysis patients. Effect on cellular immune response

The effect of blood transfusions, given in low number (less than 5), on the immune response of renal dialysis patients was studied. A significantly lowered response of lymphocytes to mitogen stimulation was observed in patients after as few as one, two or three transfusions, depending on the patient. This led to an increased delta 48/delta 0 ratio reflected by the enhanced response of the cells following delayed addition of suboptimal dose of mitogen. There was no modification of the ratio of helper/inducer to suppressor/cytotoxic T cells subsets (OKT4/OKT8). The use of such simple in vitro tests in a strict protocol of transfusions could allow an adequate follow-up thereby limiting the risks of sensitization. These results demonstrate that important phenomena affecting patients' immune response are turned on following even a low number of transfusions in the majority of uremic patients. This could probably be related to the beneficial effects of blood transfusions on the kidney allograft survival already described.

Addressing aquatic hazard classification for metals, metal compounds and alloys in marine systems

New International Maritime Organization regulations require shippers to classify all solid bulk cargo to indicate whether they are Harmful to the Marine Environment (HME). The objective of this work was to adapt the freshwater Transformation/Dissolution Protocol (T/DP) to marine water to provide a method to determine, when compared with marine Ecotoxicity Reference Values (ERVs), whether a metal-bearing substance is HME. The substances examined were: Cu2O powder; Ni metal powder; Co3O4 powder; and a Ni-Co-Fe alloy, as wire cuttings, which were the same substances examined in the freshwater T/D validation study and afforded comparisons of the reactivity, or measure of the rate and extent of metal release from the metal-bearing substances in freshwater versus marine conditions. The marine T/D method is suitable for conducting examinations of metal-bearing substances with a wide range of reactivities, from the relatively reactive Cu2O powder and the alloy to the Co3O4 powder, which was the least reactive.

Transformation/dissolution characteristics of a nickel matte and nickel concentrates for acute and chronic hazard classification

For the purposes of aquatic hazard classification under the United Nations Globally Harmonized System of Classification (UNGHS), we have examined the transformation/dissolution (T/D) characteristics of a Ni matte and 4 Ni concentrates at pH 6 using the United Nations (UN) Transformation/Dissolution Protocol (T/DP) for metals and sparingly soluble metal compounds. Among the analytes Ni, Co, and Cu, Ni was released into the T/D solutions in the highest concentrations and was thus the main driver in establishing the hazard classification. We applied an extrapolation-scaling approach to obtain concentrations of total dissolved Ni at low loadings of 0.1 and 0.01 mg/L for derivation of chronic classification outcomes in the European Union (EU) classification, labeling, and packaging (CLP) scheme. The T/D data would classify the Ni matte as Acute 2-Chronic 2 under the Globally Harmonized System (GHS) scheme, and Chronic 1 under the EU CLP. Three of the 4 Ni concentrates would classify as GHS Acute 2-Chronic 2 and EU CLP Chronic 2, whereas the 4th would classify as GHS Acute 3-Chronic 3 and EU CLP Chronic 3. In applying the critical surface area (CSA) approach to the Ni concentrates, acute and chronic hazard classification outcomes were the same as those derived from direct application of the T/D data to the GHS and EU schemes. Such agreement provided confidence that the CSA approach could yield scientifically defensible acute and chronic hazard classification outcomes.

A mechanistic understanding of the effect of Staphylococcus aureus VraS histidine kinase single point mutation on antibiotic resistance

Bacterial genomic mutations in Staphylococcus aureus (S. aureus) have been detected in isolated resistant clinical strains, yet their mechanistic effect on the development of antimicrobial resistance remains unclear. The resistance-associated regulatory systems acquire adaptive mutations under stress conditions that may lead to a gain of function effect and contribute to the resistance phenotype. Here, we investigate the effect of a single-point mutation (T331I) in VraS histidine kinase, part of the VraSR two-component system in S. aureus. VraSR senses and responds to environmental stress signals by upregulating gene expression for cell wall synthesis. A combination of enzyme kinetics, microbiological, and transcriptomic analysis revealed the mechanistic effect of the mutation on VraS and S. aureus . Michaelis Menten's kinetics show that the VraS mutation caused an increase in the autophosphorylation rate of VraS and enhanced its catalytic efficiency. The introduction of the mutation through recombineering coupled with CRISPR-Cas9 counterselection to the Newman strain wild-type (WT) genome doubled the minimum inhibitory concentration of three cell wall-targeting antibiotics. The mutation caused an enhanced S. aureus growth rate at sub-lethal doses of the antibiotics, confirming the causative effect of mutation on bacterial persistence. Transcriptomic analysis showed a genome-wide alteration in gene expression levels and protein-protein interaction network of the mutant compared to the WT strain after exposure to vancomycin. The results suggest that vraS mutation causes several mechanistic changes at the protein and cellular levels that favor bacterial survival under antibiotic stress and cause the mutation-harboring strains to become the dominant population during infection.

Importance

Rising antimicrobial resistance (AMR) is a global health problem. Mutations in the two- component system have been linked to drug- resistance in Staphylococcus aureus , yet the exact mechanism through which these mutations work is understudied. We investigated the T331I mutation in the vraS gene linked to sensing and responding to cell wall stress. The mutation caused changes at the protein level by increasing the catalytic efficiency of VraS kinase activity. Introducing the mutation to the genome of an S. aureus strain resulted in changes in the phenotypic antibiotic susceptibility, growth kinetics, and genome-wide transcriptomic alterations. By a combination of enzyme kinetics, microbiological, and transcriptomic approaches, we highlight how small genetic changes can significantly impact bacterial physiology and survival under antibiotic stress. Understanding the mechanistic basis of antibiotic resistance is crucial to guide the development of novel therapeutic agents to combat AMR.

Enantiospecific Positive Allosteric Modulation of α4β2 Nicotinic Receptor Subtypes

Nicotinic acetylcholine receptors (nAChRs) are integral to brain function, playing critical roles in cognition and reward pathways. Among these, α4β2 nAChRs are key targets for developing therapeutics to address nicotine addiction and cognitive disorders. Here, we report the synthesis, stereochemical resolution, and pharmacological evaluation of GAT2800, a racemic compound identified as a positive allosteric modulator (PAM) of α4β2 nAChRs. Enantiomeric resolution yielded the inactive S-enantiomer (GAT2801) and the pharmacologically active R-enantiomer (GAT2802), with their configurations confirmed via X-ray crystallography. Two-electrode voltage-clamp recordings from Xenopus oocytes expressing α4β2 nAChRs revealed that GAT2802, but not GAT2801, significantly potentiates current responses of both high-sensitivity (HS) (α4)2(β2)3 and low-sensitivity (LS) (α4)3(β2)2 isoforms, with EC50 values of ∼1 and ∼0.8 μM, respectively. Notably, GAT2802 enhanced ACh efficacy more profoundly in HS (α4)2(β2)3 nAChR while showing minimal activity at α3-containing nAChRs. Computational docking analyses provided insight into potential binding sites of GAT2802 at subunit interfaces within the transmembrane domain. Mutational analyses identified α4Cys233 located in the first transmembrane helix and projecting to the β2:α4 subunit transmembrane interface, as a molecular determinant for selectivity of GAT2802 for α4- over α3-containing nAChRs. Safety evaluation demonstrated negligible cellular toxicity of GAT2802 in HEK cells expressing α4β2 nAChRs and no significant developmental effects in zebrafish larvae at concentrations up to 100 μM. These findings establish GAT2802 as a promising lead compound for the development of selective α4β2 nAChR PAMs, with significant therapeutic potential for nicotine addiction and cognitive disorders.

Absence of correlation between the degree of alveolitis and antibody levels to Micropolysporum faeni

Specific IgG antibody (Ab) levels to Micropolysporum faeni (MF) antigen were measured in three study groups: 29 farmers of whom one had acute, two chronic and 26 with a past history of Farmer's lung disease (FLD), 91 clinically asymptomatic but exposed farmers and 23 unexposed donors. This study confirms the greater sensitivity of enzyme linked immunosorbent assay (ELISA) over double immunodiffusion (DID): 34 (37%) sera negative by DID were positive by ELISA and only two (4%) were positive by DID and negative by ELISA. Antibody levels to MF were higher in the serum of farmers whether symptomatic (113.2 +/- 196.1 u) or not (25.2 +/- 64.7 u) than in that of unexposed donors (1.05 +/- 1.46 u), (P less than 0.001). In a subgroup of farmers, antibody levels were compared in the serum and bronchoalveolar lavage (BAL) fluid; the levels were higher in the serum than in BAL fluids in all farmers except the only patient with acute FLD. A significant correlation was seen between Ab levels of the serum and BAL fluids. Finally, no correlation was seen between the serum antibody levels and the total number of cells or the percentage of lymphocytes found in BAL fluids, either in the subjects with a history of FLD or the asymptomatic group.

Transformation/dissolution characterization of tungsten and tungsten compounds for aquatic hazard classification

The transformation/dissolution protocol (T/DP) for metals and sparingly soluble metal compounds was applied to determine the transformation/dissolution (T/D) characteristics of yellow tungsten trioxide, WO₃ ; blue tungsten oxide, WOx, x taken as 2.9; tungsten disulphide, WS₂ ; tungsten metal, W; 3 samples of tungsten carbide, WC; sodium tungstate, Na₂ WO₄ · 2H₂ O; ammonium paratungstate (APT), (NH₄ )₁₀ (H₂ W₁₂ O₄₂ ) · 4H₂ O; and ammonium metatungstate (AMT) (NH₄ )₆ (H₂ W₁₂ O₄₀ ) · 3H₂ O. The T/D data were used to derive aquatic hazard classification outcomes under the United Nations Globally Harmonized System of Classification and Labelling of Chemicals (UN GHS) and European Union Classification, Labelling and Packaging of Substances and Mixtures (EU CLP) schemes by comparing the data with selected acute and chronic ecotoxicity reference values (ERVs) of 31 and 3.37 mg W/L, respectively. In addition to the concentration of total dissolved tungsten (W), the T/D solutions were analyzed for the concentration of the tungstate anion, because speciation can be an important factor in establishing the ecotoxicity of dissolved metals. Results show that the tungstate anion was the predominant W-bearing species in solution for all substances examined at pH 6 and 8.5. It was found that the 100 mg/L loadings of both the yellow WO₃ and the blue WOx exceeded the 31 mg/L acute ERV, so they would classify as Acute 3-Chronic 3 under the UN GHS scheme but they would not classify under the EU CLP. An effect of pH on the reactivity of the W metal was observed with 3% and 16% W dissolution at pH 6 and 8.5, respectively. Tungsten metal would not classify under either the UN GHS or EU CLP schemes nor would the WS₂ . The WCs were the least reactive in terms of the 1% or less dissolution of the contained W at pH 6. A critical surface area for WC was calculated. The sodium tungstate, APT and the AMT all yielded, at pH 8.5, total dissolved W concentrations that would result in UN GHS Acute 3-Chronic 3 classifications. Integr Environ Assess Manag 2018;14:498-508. © 2018 Her Majesty the Queen in Right of Canada. Integrated Environmental Assessment and Management © 2018 SETAC.

A mechanistic understanding of the effect of Staphylococcus aureus VraS histidine kinase single-point mutation on antibiotic resistance

Bacterial genomic mutations in Staphylococcus aureus have been detected in isolated resistant clinical strains, yet their mechanistic effect on the development of antimicrobial resistance remains unclear. Resistance-associated regulatory systems acquire adaptive mutations under stress conditions that may lead to a gain-of-function effect and contribute to the resistance phenotype. Here, we investigate the effect of a single-point mutation (T331I) in VraS histidine kinase, part of the VraSR two-component system in S. aureus. VraSR senses and responds to environmental stress signals by upregulating gene expression for cell wall synthesis. A combination of enzyme kinetics, microbiological, and transcriptomic analyses revealed the mechanistic effect of the mutation on VraS and S. aureus. Michaelis-Menten kinetics show that the VraS mutation caused an increase in the autophosphorylation rate of VraS and enhanced its catalytic efficiency. The introduction of the mutation through recombineering coupled with CRISPR-Cas9 counterselection to the Newman strain wild-type (WT) genome doubled the minimum inhibitory concentration of three cell wall-targeting antibiotics. The mutation caused an enhanced S. aureus growth rate at sub-lethal doses of the antibiotics, confirming the causative effect of the mutation on bacterial persistence. Transcriptomic analysis showed a genome-wide alteration in gene expression levels and protein-protein interaction network of the mutant compared to the WT strain after exposure to vancomycin. The results suggest that the vraS mutation causes several mechanistic changes at the protein and cellular levels that favor bacterial survival under antibiotic stress and cause the mutation-harboring strains to become the dominant population during infection.IMPORTANCERising antimicrobial resistance (AMR) is a global health problem. Mutations in the two-component system have been linked to drug resistance in Staphylococcus aureus, yet the exact mechanism through which these mutations work is understudied. We investigated the T331I mutation in the vraS gene linked to sensing and responding to cell wall stress. The mutation caused changes at the protein level by increasing the catalytic efficiency of VraS kinase activity. Introducing the mutation to the genome of an S. aureus strain resulted in changes in phenotypic antibiotic susceptibility, growth kinetics, and genome-wide transcriptomic alterations. By a combination of enzyme kinetics, microbiological, and transcriptomic approaches, we highlight how small genetic changes can significantly impact bacterial physiology and survival under antibiotic stress. Understanding the mechanistic basis of antibiotic resistance is crucial to guide the development of novel therapeutic agents to combat AMR.

The regulatory effect of histamine on the immune response: III. Defect on in vitro IgE production in atopics

Spontaneous in vitro production of IgE was found higher in a group of untreated grass sensitive atopic patients than in normal volunteers when assessed at the cellular level with a reverse hemolytic plaque assay. This study also confirmed the increase of IgE synthesis after pokeweed mitogen stimulation in non-atopic donors and its decrease in atopic patients. Moreover, in this work we looked for a potential defect in immunoregulatory functions in atopic patients toward the in vitro IgE production. Indeed, histamine is known to activate suppressor cells capable, in turn, of suppressing IgG and IgE production from normal cells. In atopic patients, histamine could activate cells capable of suppressing IgG production but not IgE. Furthermore, similar findings were found when Concanavalin A-induced suppressor cells were examined. These findings suggest (a) a defective regulatory function towards IgE in atopic patients and (b) that the same subpopulation of suppressor cells seems to be activated by histamine and ConA and defective in atopic patients.