Shelf Reagents Research Articles

Selenium Dioxide-Mediated Bromination of α,β-Unsaturated Ketones Using N-Bromosuccinimide in the Presence of p-Toluenesulfonic Acid: A Versatile Route for the Synthesis of α'-Bromo-4-arylbut-3-en-2-one and α',α'-Dibromo-4-arylbut-3-en-2-one.

An efficient method for the synthesis of α,β-unsaturated α′-bromoketones and α,β-unsaturated α′,α′-dibromoketones is described using N-bromosuccinimide (NBS) as the brominating agent mediated by selenium dioxide (SeO2) in the presence of p-toluenesulfonic acid (PTSA) monohydrate in toluene. The method is simple, employing easily available shelf reagents to afford a wide range of products in good yields. The method highlighted that simple fine-tuning of the reaction conditions and molar equivalents of the reactants easily affords either mono- or dibrominated products in excellent yields. A number of these products have not been reported in the literature. All of the reactions were carried out in gram-scale quantities.

Trifluoroacetic Acid-Mediated Oxidative Self-Condensation of Acetophenones in the Presence of SeO2: A Serendipitous Approach for the Synthesis of Fused [1,3]Dioxolo[4,5-d][1,3]dioxoles.

A method for the synthesis of fused 1,3-dioxolanes was developed by self-condensation of glyoxal generated in situ by oxidation of acetophenones with SeO2 in the presence of trifluoroacetic acid. Three molecules of the glyoxal generated by oxidation of ketone with SeO2 condensed to form architecturally novel oxygen-containing heterocycles (3a-aryldihydro-[1,3]dioxolo[4,5-d][1,3] dioxole-2,5-diyl)bis(phenylmethanones). This reaction provides a unique methodology for the construction of four C–O bonds in a concerted fashion, generating highly embedded oxygen heterocycles from readily available ketones using affordable shelf reagents and simple reaction conditions.

CAR T cells generated in situ using gene therapy in naturally activated lymph node T cells

Abstract T cells expressing chimeric antigen receptors (CAR T cells) are manufactured outside the body using non-physiological activation and in vitro culture protocols. The procedure takes 3 weeks and costs approximately $450,000 to administer. We have devised a scheme using mouse models for manufacturing CAR T cells in just 3 days employing a natural, polyclonal anti-viral immune response inside a lymph node (LN) using off the shelf reagents that can be applied widely in populations. CAR T cells emerge from the LN within a week, invade solid tumor, and eliminate the targeted antigen-positive tumor cells. Polyclonal activation of T cells is achieved by modifying the antigen presenting properties of lymph node resident professional antigen presenting cells (APC) through viral expression of allogeneic major histocompatibility antigens. The ensuing polyclonal activation occurs in the context of virus activated APC within the normal aarchitecture of the LN and confers robust T cell activation signals directing the development of cytolytic T cells. During the course of T cell activation, the T cells are transduced in situ with retroviruses encoding selected CARs. This approach could be applied to any number of different CARs to target a variety of tumors. T cells activated in the lymph node are functionally distinct from those activated using standard CAR T manufacturing protocols. We anticipate that CAR T cells generated in situ to natural stimuli will exhibit more normal immune regulatory properties that will impact their therapeutic utility. Because our approach uses off the shelf reagents and is administered using standard clinical procedures, cost to patients should be lowered and access to therapy increased.

A norovirus detection architecture based on isothermal amplification and expanded genetic systems

Noroviruses are the major cause of global viral gastroenteritis with short incubation times and small inoculums required for infection. This creates a need for a rapid molecular test for norovirus for early diagnosis, in the hope of preventing the spread of the disease. Non-chemists generally use off-the shelf reagents and natural DNA to create such tests, suffering from background noise that comes from adventitious DNA and RNA (collectively xNA) that is abundant in real biological samples, especially feces, a common location for norovirus. Here, we create an assay that combines artificially expanded genetic information systems (AEGIS, which adds nucleotides to the four in standard xNA, pairing orthogonally to A:T and G:C) with loop-mediated isothermal amplification (LAMP) to amplify norovirus RNA at constant temperatures, without the power or instrument requirements of PCR cycling. This assay was then validated using feces contaminated with murine norovirus (MNV). Treating stool samples with ammonia extracts the MNV RNA, which is then amplified in an AEGIS-RT-LAMP where AEGIS segments are incorporated both into an internal LAMP primer and into a molecular beacon stem, the second lowering background signaling noise. This is coupled with RNase H nicking during sample amplification, allowing detection of as few as 10 copies of noroviral RNA in a stool sample, generating a fluorescent signal visible to human eye, all in a closed reaction vessel.

Generation and Characterization of a Third Party GMP Grade Bank of CMV Specific T-Cells for Adoptive Immunotherapy of CMV Infections in Recipients of HSCT from Cord Blood or Seronegative Donors

Adoptive transfer of virus-specific T-cells (CTLs) derived from allogeneic HLA partially matched third party donors can also be effective in a proportion of patients developing EBV lymphomas, or infections due to CMV or adenovirus following transplants from seronegative donors. Such third party donor derived CTLs offer an off the shelf reagent for treatment of viral infections developing after transplant. However, the immunodominant cytotoxic activity exhibited by the CTLs is directed against specific epitopes of the viral protein and restricted by 1-2 HLA alleles. Therefore, it is critical that the T-cells administered from third party donors can recognize viral epitopes presented on shared HLA alleles. We have established a bank of 119 CMV specific T-cell lines (CMV CTLs) generated using autologous APCs loaded with a pool of overlapping peptides spanning the sequence of the dominant immunogenic protein CMVpp65. Each of these 119 CMV CTL lines has been characterized as to the epitope inducing T-cell response as well as the HLA allele restricting the epitope specific T-cell response. Epitopes were identified using an overlapping grid of peptide pools and the HLA restriction by cytotoxic activity against peptide loaded EBVBLCLs matched at a single HLA allele with the T-cell donor. The distribution of the common HLA alleles among the donors for these CTL lines was predominantly within the distribution of HLA allele frequencies represented in the caucasian and black populations, except for HLA A0201 and B0702, which were over represented ( 33% vs 25% and 21% vs 8.7% respectively). In 54% of the CTL lines, the immunodominant T-cell responses were restricted by HLA A0201 (25%), B0702 (21%) and B 3501-11(8%), and in the remaining 50%, the responses were restricted by other HLA class-I alleles, while only 16/119 lines (13%) were restricted by HLA class-II alleles. All 25 donors inheriting HLA B0702 (25/25) demonstrated HLA B0702 restricted CMV CTL responses, while 30/39 (77%) donors inheriting HLA A0201 and 9/19 (47%) donors inheriting HLA B3501-11 demonstrated HLA A0201 and B3501-11 restricted CMV CTL responses. Among all 9 donors co-inheriting HLA A0201 and B 0702, the immunodominant T-cell response was restricted by B0702. Among 12 donors co-inheriting A0201 and B 4401-04, 11/12 (91.6%) demonstrated immunodominant CMV CTL responses restricted by A0201; 1 donor also co-inherited HLA B0702 whose response was restricted by B0702. Therefore, an immunodominance hierarchy for HLA class-I alleles presenting the dominant CMVpp65 epitope was evident through this analysis among these 119 donors and was as follows: B 0702, A0201, B3501-11, A2601, B44, B40, B4201, A0101, B 1801. Strikingly, only 1 of 119 donors demonstrated T-cell responses restricted by A1101; a commonly inherited HLA class –I allele. In a series of 239 consecutive HLA matched related or unrelated transplants (MUD) and 137 HLA mismatched unrelated (MMUD) transplants, and 100 cord blood transplants conducted at our center, in 86%, 89% and 80% of the cases respectively, we could identify a CMV CTL line restricted by a shared HLA allele and matched at 2-3 alleles within this GMP grade CTL bank that would be immediately available for treatment of CMV infection. Appropriately restricted CMV CTLs would only be available in 60-70% of MMUD transplant and none of the cord blood transplants without this approach. This CMV CTL bank therefore represents a readily available clinical reagent for the treatment of resistant CMV infections developing in post transplant patients. The characterization of the CTLs has also enabled the further elucidation of immunodominant CMVpp65 epitopes and hierarchies. Since we have previously shown that CMV CTLs can be generated against subdominant epitopes presented by both common HLA alleles as well as less prevalent HLA alleles using a panel of artificial antigen presenting cells (AAPCs), expansion of this bank using T-cell sensitized against CMVpp65 presented on such AAPCs should broaden the applicability of this bank to all HSCT recipients. Disclosures: No relevant conflicts of interest to declare.

Generation and Characterization Of a Third Party GMP Grade Bank Of CMV Specific T-Cells For Adoptive Immunotherapy Of CMV Infections In Recipients Of HSCT From Cord Blood Or Seronegative Donors

Adoptive transfer of virus-specific T-cells (CTLs) derived from allogeneic HLA partially matched third party donors can also be effective in a proportion of patients developing EBV lymphomas, or infections due to CMV or adenovirus following transplants from seronegative donors. Such third party donor derived CTLs offer an off the shelf reagent for treatment of viral infections developing after transplant. However, the immunodominant cytotoxic activity exhibited by the CTLs is directed against specific epitopes of the viral protein and restricted by 1-2 HLA alleles. Therefore, it is critical that the T-cells administered from third party donors can recognize viral epitopes presented on shared HLA alleles. We have established a bank of 119 CMV specific T-cell lines (CMV CTLs) generated using autologous APCs loaded with a pool of overlapping peptides spanning the sequence of the dominant immunogenic protein CMVpp65. Each of these 119 CMV CTL lines has been characterized as to the epitope inducing T-cell response as well as the HLA allele restricting the epitope specific T-cell response. Epitopes were identified using an overlapping grid of peptide pools and the HLA restriction by cytotoxic activity against peptide loaded EBVBLCLs matched at a single HLA allele with the T-cell donor.The distribution of the common HLA alleles among the donors for these CTL lines was predominantly within the distribution of HLA allele frequencies represented in the caucasian and black populations, except for HLA A0201 and B0702, which were over represented ( 33% vs 25% and 21% vs 8.7% respectively). In 54% of the CTL lines, the immunodominant T-cell responses were restricted by HLA A0201 (25%), B0702 (21%) and B 3501-11(8%), and in the remaining 50%, the responses were restricted by other HLA class-I alleles, while only 16/119 lines (13%) were restricted by HLA class-II alleles.All 25 donors inheriting HLA B0702 (25/25) demonstrated HLA B0702 restricted CMV CTL responses, while 30/39 (77%) donors inheriting HLA A0201 and 9/19 (47%) donors inheriting HLA B3501-11 demonstrated HLA A0201 and B3501-11 restricted CMV CTL responses. Among all 9 donors co-inheriting HLA A0201 and B 0702, the immunodominant T-cell response was restricted by B0702. Among 12 donors co-inheriting A0201 and B 4401-04, 11/12 (91.6%) demonstrated immunodominant CMV CTL responses restricted by A0201; 1 donor also co-inherited HLA B0702 whose response was restricted by B0702. Therefore, an immunodominance hierarchy for HLA class-I alleles presenting the dominant CMVpp65 epitope was evident through this analysis among these 119 donors and was as follows: B 0702, A0201, B3501-11, A2601, B44, B40, B4201, A0101, B 1801. Strikingly, only 1 of 119 donors demonstrated T-cell responses restricted by A1101; a commonly inherited HLA class –I allele.In a series of 239 consecutive HLA matched related or unrelated transplants (MUD) and 137 HLA mismatched unrelated (MMUD) transplants, and 100 cord blood transplants conducted at our center, in 86%, 89% and 80% of the cases respectively, we could identify a CMV CTL line restricted by a shared HLA allele and matched at 2-3 alleles within this GMP grade CTL bank that would be immediately available for treatment of CMV infection. Appropriately restricted CMV CTLs would only be available in 60-70% of MMUD transplant and none of the cord blood transplants without this approach. This CMV CTL bank therefore represents a readily available clinical reagent for the treatment of resistant CMV infections developing in post transplant patients. The characterization of the CTLs has also enabled the further elucidation of immunodominant CMVpp65 epitopes and hierarchies. Since we have previously shown that CMV CTLs can be generated against subdominant epitopes presented by both common HLA alleles as well as less prevalent HLA alleles using a panel of artificial antigen presenting cells (AAPCs), expansion of this bank using T-cell sensitized against CMVpp65 presented on such AAPCs should broaden the applicability of this bank to all HSCT recipients. Disclosures:No relevant conflicts of interest to declare.

Next-Generation Sequencing Strategies Enable Routine Detection of Balanced Chromosome Rearrangements for Clinical Diagnostics and Genetic Research

The contribution of balanced chromosomal rearrangements to complex disorders remains unclear because they are not detected routinely by genome-wide microarrays and clinical localization is imprecise. Failure to consider these events bypasses a potentially powerful complement to single nucleotide polymorphism and copy-number association approaches to complex disorders, where much of the heritability remains unexplained. To capitalize on this genetic resource, we have applied optimized sequencing and analysis strategies to test whether these potentially high-impact variants can be mapped at reasonable cost and throughput. By using a whole-genome multiplexing strategy, rearrangement breakpoints could be delineated at a fraction of the cost of standard sequencing. For rearrangements already mapped regionally by karyotyping and fluorescence in situ hybridization, a targeted approach enabled capture and sequencing of multiple breakpoints simultaneously. Importantly, this strategy permitted capture and unique alignment of up to 97% of repeat-masked sequences in the targeted regions. Genome-wide analyses estimate that only 3.7% of bases should be routinely omitted from genomic DNA capture experiments. Illustrating the power of these approaches, the rearrangement breakpoints were rapidly defined to base pair resolution and revealed unexpected sequence complexity, such as co-occurrence of inversion and translocation as an underlying feature of karyotypically balanced alterations. These findings have implications ranging from genome annotation to de novo assemblies and could enable sequencing screens for structural variations at a cost comparable to that of microarrays in standard clinical practice.

Positional proteomics: preparation of amino-terminal peptides as a strategy for proteome simplification and characterization

We describe a protocol for selective extraction of the amino (N)-terminal-most peptide of a protein or a mixture of proteins after proteolysis. The first stage of the protocol blocks the free amino groups alpha and epsilon (the latter being lysyl residues) on the intact proteins by acetylation. In the second stage, proteolysis of the acetylated proteins yields a mixture of N-terminally acetylated (true N-terminal) and non-acetylated (internal and carboxy-terminal) peptides. Affinity capture of peptides bearing free amino groups using an immobilized amine-reactive reagent removes internal peptides from the mixture. The unbound fraction is highly enriched in N-terminal peptides, which can be analyzed without further treatment. This method is compatible with a range of proteolytic enzymes and fragmentation methods, and should take 2 d to complete. The N-terminal peptides can then be analyzed by mass spectrometry. This low cost, rapid method is readily adopted using off the shelf reagents.

The isotopic composition and atomic weight of molybdenum

The isotopic composition of molybdenum in a shelf reagent standard (MoO 3, 99.99%), 13 molybdenites, and three iron meteorites has been determined with a thermal ionization mass spectrometer. No especially-evident variations of molybdenum isotopes among these samples have been found. The mass fractionation of molybdenum occurring in isotopes during the measurements is discussed and our preferred natural abundances of molybdenum isotopes are: 92Mo, 14.7287 ± 0.0010; 94Mo, 9.2118 ± 0.0006; 95Mo, 15.8935 ± 0.0011; 96Mo, 16.6731 ± 0.0011; 97Mo, 9.5692 ± 0.0007; 98Mo, 24.2289 ± 0.0017; 100Mo, 9.6950 ± 0.0007. Thus, the atomic weight of molybdenum is 95.9415 ± 0.0001 (the value currently accepted by IUPAC [IUPAC Inorganic Chemistry Division, Pure Appl. Chem., 63 (1991) 991] is 95.94 ± 0.01). The uncertainties correspond to the 95% confidence limit calculated from all the terrestrial and meteoritic samples.

Binding of Bacteria to Lymphocyte Subpopulations

Publisher Summary Both in humans and in mice, it has been possible to map the lymphocyte subpopulations using bacteria as specific membrane markers. All human B cells, normal or leukemic, bind Brucella melitensis as well as other human pathogens from the genus Brucella, while T cells do not bind these bacteria. By using four strains of bacteria, B. melitensis, A. hinshawii, B. globigii, and S. schottmulleri, in addition to B cells (Bm+), two B- and four T-cell subpopulations have been identified—which were given arbitrary numbers, B1, B2, and T1–T4. Three B cell subpopulations, B1–B3, and three T cell subpopulations, T1–T3, were identified in the mouse spleen using a minimum of four bacteria: B. melitensis, A. hinshawii, E. coli-2, and E. coli-3. As the function of B cells is definitely different from that of T cells, the existence of B. melitensis as a B cell marker suggested that the lymphocyte subpopulations identified by bacterial adherence are functionally different. Experiments with B. melitensis and with a mutant of E. coli suggested that there may be lectins on the lymphocyte membrane that interact with carbohydrates on the bacteria, an interaction that can be inhibited by certain monosaccharides or by the specific lipopolysaccharides (LPS). Bacteria bind consistently to lymphocytes, and their binding properties are not affected by heating or formaldehyde fixation. These properties have allowed their use as shelf reagents in stained smears prepared from peripheral blood or from bone marrow. The use of bacteria as markers of lymphocyte subpopulations is significant for a few reasons—bacteria are stable shelf reagents, easy to prepare, and store.. The use of bacteria in blood smears offers the possibility of morphologic examination of the lymphocytes and of obtaining a permanent record.

The isotopic composition and the atomic weight of zirconium

The isotopic composition of zirconium in the normal shelf reagent and in two terrestrial rock standards, W-1 and G-2, has been determined. In the course of this study, the mass spectrometric measurements were checked by artificla mixtures of 90Zr-, 91Zr-, 92Zr- and 94Zr-enriched isotopes. The absolute isotopic abundance obtained in this work is as follows (atom%); 90Zr: 51.449 ± 0.059; 91Zr: 11.320 ± 0.015; 92Zr: 17.189 ± 0.021; 94Zr: 17.283 ± 0.021; and 96Zr: 2.759 ± 0.004. Because of the higher accuracy, these abundances should replace the currently accepted values. The corresponding atomic weight of zirconium was calcualted to be 91.219. This shows good agreement with the currently accepted value of 91.22 by IUPAC (1975), although the isotopic composition differs slightly from the IUPAC “intrim” values. From nine chondrites, belonging to various classes, zirconium was extracted and the isotopic composition was determined. By the present technique, the limit of the experimental error for a single measurement of each sample, 2σ ≈ 0.5%, prevents detection of possible incomplete mixing during and after nucleosynthesis and following the formation of the solar system.

Measurements of the isotopic ratios of nickel in iron meteorites using nickel carbonyl

The isotopic ratios of nickel in a shelf reagent, a dunite and three meteoritic irons were measured. Ni(CO)4 was synthesized from samples and introduced into a mass spectrometer in gaseous form. All the precisions of the isotopic ratio measurements were within one percent which was better than those of previous studies by furnace methods. The relative abundance of 64Ni was lower than that given by WHITE and CAMERON by 20%. There was no significant difference in the isotopic ratios of 60Ni/58Ni, 61Ni/58Ni, 62Ni/58Ni and 64Ni/58Ni between samples analyzed. The present method needs further improvements to remove troubles caused by the decomposition of Ni(CO)4 in the ion source of the mass spectrometer.

The application of thiosalts in analysis : A new scheme of qualitative analysis - part a

1. A new scheme of qualitative analysis for mixtures containing the common as well as the so-called “rare” elements has been discussed. 2. The new scheme is based upon the immediate formation of thiosalts by metals of the arsenic group (and vanadium) on adding concentrated ammonium sulphide solution and the subsequent decomposition of the thiosalts with excess of hydrochloric acid. 3. This scheme has the following advantages over the classical scheme now in use: a. The slow precipitation of the copper and arsenic groups by hydrogen sulphide in hydrochloric acid solution has been replaced by a more simple and rapid method of precipitating the sulphides completely. A considerable saving of time taken in analysis is thus effected. b. The use of the hydrogen sulphide gas which is extremely inconvenient especially in large classes of students, has been eliminated and its place has been taken by concentrated ammonium sulphide—a reagent which can be easily prepared and used as a shelf reagent. c. The use of yellow ammonium sulphide which does not give a satisfactory separation of the copper group from the arsenic group has been eliminated. d. As the main features of the new scheme are similar to those of the classical scheme the student who has been trained in the old technique can take to the new scheme without much difficulty.