NeoSplice: a bioinformatics method for prediction of splice variant neoantigens.

Motivation: Splice variant neoantigens are a potential source of tumor-specific antigen (TSA) that are shared between patients in a variety of cancers, including acute myeloid leukemia. Current tools for genomic prediction of splice variant neoantigens demonstrate promise. However, many tools have not been well validated with simulated and/or wet lab approaches, with no studies published that have presented a targeted immunopeptidome mass spectrometry approach designed specifically for identification of predicted splice variant neoantigens.

Entinostat induces antitumor immune responses through immune editing of tumor neoantigens.

Although immune-checkpoint inhibitors (ICIs) have been a remarkable advancement in bladder cancer treatment, the response rate to single-agent ICIs remains suboptimal. There has been substantial interest in the use of epigenetic agents to enhance ICI efficacy, although precisely how these agents potentiate ICI response has not been fully elucidated. We identified entinostat, a selective HDAC1/3 inhibitor, as a potent antitumor agent in our immune-competent bladder cancer mouse models (BBN963 and BBN966).

Landscape and selection of vaccine epitopes in SARS-CoV-2.

Background: Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4 T cell, and CD8 T cell stimulation. The rationale for this design was to drive both humoral and cellular immunity with high specificity while avoiding undesired effects such as antibody-dependent enhancement (ADE).

Methods: We explored the set of computationally predicted SARS-CoV-2 HLA-I and HLA-II ligands, examining protein source, concurrent human/murine coverage, and population coverage.

Landscape and Selection of Vaccine Epitopes in SARS-CoV-2.

There is an urgent need for a vaccine with efficacy against SARS-CoV-2. We hypothesize that peptide vaccines containing epitope regions optimized for concurrent B cell, CD4 T cell, and CD8 T cell stimulation would drive both humoral and cellular immunity with high specificity, potentially avoiding undesired effects such as antibody-dependent enhancement (ADE). Additionally, such vaccines can be rapidly manufactured in a distributed manner.

Atmospheric depositions affect the growth patterns of Scots pines (Pinus sylvestris L.)-a long-term cause-effect monitoring study using biomarkers.

Recording the causes, effects, and effect mechanisms of vegetation health is crucial to understand process-pattern interactions in ecosystem processes. NO and SO in the form of air pollution are both triggers and sources of vegetation health that can have an effect on the local or the global level and whose impacts need to be monitored. In this study, the growth patterns in Scots pines (Pinus sylvestris L.

Metal complex SERMs (selective oestrogen receptor modulators). The influence of different metal units on breast cancer cell antiproliferative effects.

The selective oestrogen receptor modulator tamoxifen is a leading agent in the adjuvant treatment of breast cancer. Several organometallic moieties have been vectorised with tamoxifen, in order to improve on the latter's antiproliferative properties by the addition of a potentially cytotoxic moiety, and have been evaluated versus both oestrogen receptor positive (MCF7) and oestrogen receptor negative (MDA-MB231) breast cancer cells. For tamoxifen analogues with ((R,R)-trans-1,2-diaminocyclohexane)platinum(II), cyclopentadienyl rhenium tricarbonyl, and ruthenocene tethers, there was no enhancement of the antiproliferative effect on oestrogen receptor positive cells, nor any cytotoxic effect on oestrogen receptor negative cells, while those containing cyclopentadienyl titanium dichloride showed an oestrogenic effect.

The chemistry of the fac-[Re(CO)2(NO)]2+ fragment in aqueous solution.

The anions [ReX3(CO)2(NO)]- (with X = Cl, 1; X = Br, 2) have been prepared with different counterions. Complex 1 was found to lose its chloride ligands in water within 24 h. The [Re(H2O)3(CO)2(NO)]2+ cation obtained after hydrolysis is a strong acid, which consequently undergoes a slow condensation reaction in water to form the very stable [Re(mu3-O)(CO)2(NO)]4 cluster 4 at pH > 2, that precipitates from the aqueous solution and is insoluble also in organic solvents.

Alpha-amino acids with metallocenyl side chains.

A straightforward method for the synthesis of enantiomerically pure bis(valine)metallocenes is presented. Derivatives of lithium cyclopentadienylvaline 1a, b were obtained by addition of the (R)- or (S)-Schöllkopf reagents to 6,6-dimethylfulvene as single enantiomers and gave with FeCl2 or [RuCl2(dmso)4] the chiral metallocenes [Fe[C5H4-CMe2-[C4H2N2(OMe)2iPr]]2] (2a, b) and [Ru[C5H4-CMe2-[C4H2N2(OMe)2iPr]]2] (3a, b). Complex 2b was hydrolyzed to the ferrocenylene-bis(valine-methylester) [[Fe[C5H4-CMe2-CH(NH3+)COOMe]2]2+(Cl-)2] (7) without racemization.

Bioorganometallic Chemistry - Transition Metal Complexes with α-Amino Acids and Peptides.

A new, interdisciplinary research area has emerged known as bioorganometallic chemistry. It focuses on the introduction of organometallic fragments into biomolecules (see, for example, structure on the right). "Classical" α-amino acid and peptide ligands have proven particularly versatile, and provide access to compounds that display interesting stereochemistry.

Facile Synthesis of Cyclic Tetrapeptides from Nonactivated Peptide Esters on Metal Centers.

The cyclization of dipeptide esters of α-, β-, γ-, and δ-amino acids can be achieved by using Ni , Pd , or Cu templates. The structure of one of the complexes (1) obtained, which was determined by X-ray crystallography, reveals that the anions form layers and are linked to water molecules by hydrogen bonds.

Synthesis, Structure, and Magnetic Properties of Transition Metal Complexes of the Nitroxide 2,5-Dihydro-4,5,5-trimethyl-2,2-bis(2-pyridyl)imidazole-1-oxyl.

With the radical 2,5-dihydro-4,5,5-trimethyl-2,2-bis(2-pyridyl)imidazole-1-oxyl (L) a series of transition metal complexes have been prepared: [ML(2)](SbF(6))(2) with M(2+) = Mn(2+) (1), Fe(2+) (2), Co(2+) (3), Ni(2+) (4), Cu(2+) (5), and Zn(2+) (6), Cu(L)(Cl)(2)(MeOH) (7), and Cu(L)SO(4).H(2)O (8). The structures of 1, 3, and 6 were determined by X-ray structural analyses.