Forward Vaccinology: CTL Targeting Based upon Physical Detection of HLA-Bound Peptides

Vaccine-elicited cytotoxic T lymphocytes (CTL) recognizing conserved fragments of a pathogen’s proteome could greatly impact infectious diseases and cancers. Enabling this potential are recent advances in mass spectrometry that identify specific target peptides among the myriad HLA-bound peptides on altered cells. Ultrasensitivity of these physical detection methods allows for the direct assessment of peptide presentation on small numbers of tissue-derived cells. In addition, concurrent advances in immunobiology suggest ways to induce CTLs with requisite functional avidity and tissue deployment. Elicitation of high-avidity resident-memory T cells through vaccination may shift the vaccinology paradigm both for preventive and therapeutic approaches to human disease control

Regulation of prostaglandin synthesis and cell adhesion by a tryptophan catabolizing enzyme

BACKGROUND: The tryptophan catabolizing enzyme, indoleamine 2,3, dioxygenase (IDO) is one of two mammalian enzymes, which can catabolize the rarest essential amino acid, tryptophan. IDO is inducible by cytokines such as interferon-γ and plays a role in inflammation and maternal tolerance of fetal allografts, although its exact mode of action is unclear. Therefore, we investigated the circumstances under which IDO is expressed in vitro together with the effects of overexpression of IDO on the growth and morphology of cells. RESULTS: Overexpression of IDO in the murine macrophage cell line RAW 264.7 and the murine fibrosarcoma cell line MC57, resulted in the growth of macroscopic cell foci, with altered cell adhesion properties. The expression of IDO was also detected during adhesion of wild type, nontransfected cells in tissue culture to standard cell growth substrates. Inhibition of this expression, likewise resulted in alterations in cell adhesion. Overexpression of IDO or inhibition of endogenous IDO expression was accompanied by changes in metalloproteinase expression and also in the expression and activity of the cyclooxygenase enzymes. In the case of RAW cells, IDO effects on cell growth could be reversed by adding back prostaglandins. CONCLUSIONS: These results suggest that catabolism of the rarest essential amino acid may regulate processes such as cell adhesion and prostaglandin synthesis

Reactor designs and configurations for biological and bioelectrochemical C1 gas conversion: a review

Microbial C1 gas conversion technologies have developed into a potentially promising technology for converting waste gases (CO2, CO) into chemicals, fuels, and other materials. However, the mass transfer constraint of these poorly soluble substrates to microorganisms is an important challenge to maximize the efficiencies of the processes. These technologies have attracted significant scientific interest in recent years, and many reactor designs have been explored. Syngas fermentation and hydrogenotrophic methanation use molecular hydrogen as an electron donor. Furthermore, the sequestration of CO2 and the generation of valuable chemicals through the application of a biocathode in bioelectrochemical cells have been evaluated for their great potential to contribute to sustainability. Through a process termed microbial chain elongation, the product portfolio from C1 gas conversion may be expanded further by carefully driving microorganisms to perform acetogenesis, solventogenesis, and reverse -oxidation. The purpose of this review is to provide an overview of the various kinds of bioreactors that are employed in these microbial C1 conversion processes.This study was conducted in collaboration with researchers from four different institu tions (Dokuz Eylul University, Turkey; University of Minho, Portugal; Izmir Democracy University, Turkey, and University of A Coruña, Spain), who were supported by the following funding bodies: A.A. [Dokuz Eylul University, Scientific Research Foundation (DEU-BAP) (#2011.KB.FEN.046) and TUBİTAK (#119R029)]; L.P. [Portuguese Foundation for Science and Technology (FCT) (UIDB/04469/2020), and FCT and European Social Fund (POPH-QREN) (POCI-01-0145-FEDER 031377)]; T.K. [TUBİTAK-CAYDAG (118Y305)]; and H.N.A. [Xunta de Galicia (ED431C 2021/55)].A.A. acknowledges the support by Dokuz Eylul University, Scientific Research Foundation (DEU-BAP), Turkey, for the award on (#2011.KB.FEN.046) “Direct Electricity Generation from Treatment Plant Sludges by using MFCs” research project. A.A. acknowledges TUBİTAK for the support on #119R029 “Sustainable Energy Recovery from Treatment plant sludge, green waste and olive pomace via gasification process: Investigation of beneficial usage alternatives of gasification by-products”. L.P. acknowledges the Portuguese Foundation for Science and Technol ogy (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit. Also, the financial sup port from Portuguese Foundation for Science and Technology (FCT) and European Social Fund (POPH-QREN) through the project INNOVsyn - Innovative strategies for syngas fermentation (POCI-01-0145-FEDER-031377) are gratefully acknowledged. T.K. acknowledges the support from The Scientific and Technological Research Council of Turkey (TUBITAK-CAYDAG) (project no: 118Y305). H.N.A. thanks the Xunta de Galicia (Spain) for his postdoctoral fellowship (ED481D 2019/033). H.N.A., belonging to the BIOENGIN group of the UDC, also acknowledges Xunta de Galicia for recognizing the group as a competitive Reference Research Group (GRC) (ED431C 2021/55).info:eu-repo/semantics/publishedVersio

Molecular Detection of Targeted Major Histocompatibility Complex I-Bound Peptides Using a Probabilistic Measure and Nanospray MS3 on a Hybrid Quadrupole-Linear Ion Trap

A nanospray MS3 method deployed on a quadrupole linear ion trap hybrid can detect targeted peptides with high dynamic range and high sensitivity from complex mixtures without separations. The method uses a recognition algorithm that is a modification of the relative (Kullback−Leibler, KL) entropy characterization of probabilistic distance to detect if reference MS3 fragmentation patterns are components of acquired MS3 spectra. The recognition reflects the probabilistic structure of physical MS measurements unlike the Euclidean or inner product metrics widely used for comparing spectra. It capably handles spectra with a significant chemical ion background in contrast to the Euclidean metric or the direct relative entropy. The full nanospray MS3 method allows both the detection and quantitation of targets without the need to obtain isotopically labeled standards. By avoiding chromatographic separations and its associated surface losses, the detection can be applied to complex samples on a very limited material scale. The methodology is illustrated by applications to the medically important problem of detecting targeted major histocompatibility complex (MHC) I associated peptides extracted from limited cell numbers

Minimum Configuration Insensitive Multifunctional Current-Mode Biquad Using Current Conveyors and All-Grounded Passive Components

This paper proposes a new current conveyorbased high-output impedance single-input three-output current mode filter with minimum configuration. It contains two dual output second generation current conveyors, one third generation dual output current conveyor, and four grounded resistors and capacitors. The circuit simultaneously provides low-pass, band-pass, and high-pass filtering outputs, without any passive component matching conditions and restrictions on input signals. Additionally, the proposed circuit offers following advantages: Minimum active and passive element count, high output and low input impedances, suitable for cascading identical currentmode sections, all passive elements are grounded (no virtual grounding), low natural frequency and Q-factor sensitivities. The influences of non-ideal current conveyors on the proposed circuit are researched in the last

{N,N-Bis 2-(Diphenylphosphanyl)Ethyl Aniline}(Eta(2)-Dibenzylideneaceton E)Palladium(0)

In the title complex, [Pd(C34H33NP2)(C17H14O)], the Pd-0 atom is coordinated in a trigonal planar geometry formed by two P atoms of a bis[(diphenylphosphino)ethyl] aniline ligand and a C=C (eta(2)) bond involving the C atoms that are in the alpha,beta positions relative to the central ketone of the dibenzylideneacetone ligand.Robert A. Welch Foundation F-1631National Science Foundation CHE-0741973, CHE-0847763Texas Higher Education Coordinating Board 01916-090-2010American Heart Association 0765078YUT-AustinICDDSigma-Xi, the Scientific Research SocietyChemistryBiochemistr

PB1-F2 Finder: scanning influenza sequences for PB1-F2 encoding RNA segments

<p>Abstract</p> <p>Background</p> <p>PB1-F2 is a major virulence factor of influenza A. This protein is a product of an alternative reading frame in the PB1-encoding RNA segment 2. Its presence of is dictated by the presence or absence of premature stop codons. This virulence factor is present in every influenza pandemic and major epidemic of the 20th century. Absence of PB1-F2 is associated with mild disease, such as the 2009 H1N1 (“swine flu”).</p> <p>Results</p> <p>The analysis of 8608 segment 2 sequences showed that only 8.5% have been annotated for the presence of PB1-F2. Our analysis indicates that 75% of segment 2 sequences are likely to encode PB1-F2. Two major populations of PB1-F2 are of lengths 90 and 57 while minor populations include lengths 52, 63, 79, 81, 87, and 101. Additional possible populations include the lengths of 59, 69, 81, 95, and 106. Previously described sequences include only lengths 57, 87, and 90. We observed substantial variation in PB1-F2 sequences where certain variants show up to 35% difference to well-defined reference sequences. Therefore this dataset indicates that there are many more variants that need to be functionally characterized.</p> <p>Conclusions</p> <p>Our web-accessible tool PB1-F2 Finder enables scanning of influenza sequences for potential PB1-F2 protein products. It provides an initial screen and annotation of PB1-F2 products. It is accessible at <url>http://cvc.dfci.harvard.edu/pb1-f2</url>.</p

Elicitation from virus-naive individuals of cytotoxic T lymphocytes directed against conserved HIV-1 epitopes

Cytotoxic T lymphocytes (CTL) protect against viruses including HIV-1. To avoid viral escape mutants that thwart immunity, we chose 25 CTL epitopes defined in the context of natural infection with functional and/or structural constraints that maintain sequence conservation. By combining HLA binding predictions with knowledge concerning HLA allele frequencies, a metric estimating population protection coverage (PPC) was computed and epitope pools assembled. Strikingly, only a minority of immunocompetent HIV-1 infected individuals responds to pools with PPC >95%. In contrast, virus-naive individuals uniformly expand IFNγ producing cells and mount anti-HIV-1 cytolytic activity. This disparity suggests a vaccine design paradigm shift from infected to normal subjects

Origin of Native Driving Force in Protein Folding

We derive an expression with four adjustable parameters that reproduces well the 20x20 Miyazawa-Jernigan potential matrix extracted from known protein structures. The numerical values of the parameters can be approximately computed from the surface tension of water, water-screened dipole interactions between residues and water and among residues, and average exposures of residues in folded proteins.Comment: LaTeX file, Postscript file; 4 pages, 1 figure (mij.eps), 2 table

Direct Identification of an HPV-16 Tumor Antigen from Cervical Cancer Biopsy Specimens

Persistent infection with high-risk human papilloma viruses (HPV) is the worldwide cause of many cancers, including cervical, anal, vulval, vaginal, penile, and oropharyngeal. Since T cells naturally eliminate the majority of chronic HPV infections by recognizing epitopes displayed on virally altered epithelium, we exploited Poisson detection mass spectrometry (MS3) to identify those epitopes and inform future T cell-based vaccine design. Nine cervical cancer biopsies from HPV-16 positive HLA-A*02 patients were obtained, histopathology determined, and E7 oncogene PCR-amplified from tumor DNA and sequenced. Conservation of E7 oncogene coding segments was found in all tumors. MS3 analysis of HLA-A*02 immunoprecipitates detected E711–19 peptide (YMLDLQPET) in seven of the nine tumor biopsies. The remaining two samples were E711–19 negative and lacked the HLA-A*02 binding GILT thioreductase peptide despite possessing binding-competent HLA-A*02 alleles. Thus, the conserved E711–19 peptide is a dominant HLA-A*02 binding tumor antigen in HPV-16 transformed cervical squamous and adenocarcinomas. Findings that a minority of HLA-A*02:01 tumors lack expression of both E711–19 and a peptide from a thioreductase important in processing of cysteine-rich proteins like E7 underscore the value of physical detection, define a potential additional tumor escape mechanism and have implications for therapeutic cancer vaccine development