Discovery of putative breast cancer antigens using an integrative platform of genomics‐driven immunoproteomics

Recent advances in cancer immuno‐therapeutics such as checkpoint inhibitors, chimeric antigen‐receptor T cells, and tumor infiltrating T cells (TIL) are now significantly impacting cancer patients in a positive manner. Although very promising, reports indicate no more than 25% of cases result in complete remission. One of the limitations of these treatments is the identity of putative cancer antigens in each patient, as it is technically challenging to identify cancer antigens in a rapid fashion. Thus, identification of cancer antigens followed by targeted treatment will increase the efficacy of cancer immunotherapies. To achieve this goal, a combined technologies platform of deep genomic sequencing and personalized immune assessment was devised, termed G enomics D riven I mmunoproteomics (GDI). Using this technological platform, we report the discovery of 149 tumor antigens from human breast cancer patients. Significant number of these putative cancer antigens arise from single nucleotide variants (SNVs), as well as insertions and deletions that results into frame‐shift mutations. We propose a general model of anti‐cancer immunity and suggest that the GDI platform may help identify patient‐specific tumor antigens in a timely fashion for precision immunotherapies.     

Evaluation of Pseudomonas sp. PM 11 and Vibrio fluvialis PM 17 on immune indices of tiger shrimp, Penaeus monodon

Occurrence of widespread epizootics among cultured stock of shrimp has put research programmes on preventive approaches such as application of probiotics on a high priority in aquaculture. In the present study two bacteria, Pseudomonas sp. PM 11 and Vibrio fluvialis PM 17 were selected as candidate probionts from a pool of bacteria isolated from gut of farm reared sub-adult shrimp and tested for their effect on the immunity indicators of tiger shrimp. Sub-adult shrimp, weighing 14 to 22 g were treated in separate experiments with Pseudomonas sp. PM 11 and V. fluvialis PM 17 at 10(3) bacterial cells ml(-1) in the experimental shrimp culture tanks. One set of experimental animals was treated every 3 days and another set of animals every 7 days with each of the candidate probionts. Estimation of immunological indicators such as haemocyte counts, phenol oxidase and antibacterial activity showed declining trends. The haemocyte counts dropped from 31 x 10(3) to 65 x 10(3) ml(-1) on the first day to 4-16 x 10(3) ml(-1) on the 45th day. Similarly, the phenol oxidase activity declined from 12-32 units on the first day to 11-14 units on 45th day of the experiment. Antibacterial activity of haemolymph reduced to 46-67 percent on the 45th day of the experiment. The results of the study suggest that, the criteria used for the selection of putative probiotic strains in the present study, such as predominant growth on primary isolation media, ability to produce extracellular enzymes and siderophores, did not bring about the desired effect in vivo and improve the immune system in shrimp. Hence, new protocols have to be evolved for selection of microbe(s) as putative probiotics and that, detailed understanding of proven probiotics, employed presently on empirical basis may provide a clue on the selection procedure.     

Alterations in tumour suppressor gene p53 in human gliomas from Indian patients

Alterations in the tumour suppressorp53 gene are among the most common defects seen in a variety of human cancers. In order to study the significance of thep53 gene in the genesis and development of human glioma from Indian patients, we checked 44 untreated primary gliomas for mutations in exons 5–9 of thep53 gene by PCR-SSCP and DNA sequencing. Sequencing analysis revealed six missense mutations. The incidence of p53 mutations was 13⋅6% (6 of 44). All the six mutations were found to be located in the central core domain of p53, which carries the sequence-specific DNA-binding domain. These results suggest a rather low incidence but a definite involvement of p53 mutations in the gliomas of Indian patients.     

Crystal growth in aqueous hydrofluoric acid and (HF)x · pyridine solutions: syntheses and crystal structures of [Ni(H2O)6][MF6] (M = Ti, Zr, Hf) and Ni3(py)12F6 · 7H2O

The syntheses and structures of [Ni(H₂O)₆]²⁺[MF₆]²⁻ (M = Ti,Zr,Hf) and Ni₃(py)₁₂F₆·7H₂O are reported. The former three compounds are isostructural, crystallizing in the trigonal space group (No. 148) with Z = 3. The lattice parameters are a = 9.489(4), C = 9.764(7) Å, with V = 761(1) ų for Ti; a = 9.727(2), C = 10.051(3) Å, with V = 823.6(6) ų for Zr; and a = 9.724(3), C = 10.028(4)Å, with V = 821.2(8)ų for Hf. The structures consist of discrete [Ni(H₂O)₆]²⁺ and [MF₆]²⁻ octahedra joined by O---HF hydrogen bond Large single crystals were grown in an aqueous hydrofluoric acid solution. Ni₃(py)₁₂F₆·7H₂O crystallizes in the monoclinic space group I2/a (No. 15) with Z = 4. The lattice parameters are a = 16.117(4), B = 8.529(3), C = 46.220(7) Å, β = 92.46(2)°, and V = 6348(5) ų. The structure consists of discrete Ni(py)₄F₂ octahedra linked through H---O---HF and H---O---HO hydrogen bonding interactions. Single c were grown from a (HF)_x·pyridine/pyridine/water solution.     

The effect of INA [(R)-1-O-(1-pyrenylmethyl)glycerol] insertions on the structure and biological activity of a G-quadruplex from a critical KRAS G-rich sequence

Quadruplex-forming oligonucleotides containing INA [(R)-1-O-(1-pyrenylmethyl)glycerol] insertions have been designed and studied for their capacity to inhibit the expression of the KRAS oncogene in pancreatic adenocarcinoma cells. It is found that INA can influence the folding topology of the G-quadruplex. The oligonucleotides forming the most stable G-quadruplex (ODN-637) is found to exhibit the highest bioactivity.     

Genetic variability and population structure in a collection of inbred lines derived from a core germplasm of castor

Castor (Ricinus communis L.) is an industrially important oilseed crop and is the only source of an unusual fatty acid, ricinoleic acid in plant species. The castor oil and its products have numerous industrial uses including biofuel; hence, the demand for castor oil is ever increasing globally. Current productivity levels in castor are inadequate to meet the requirement, which underscores the need for breeding high yielding cultivars with better adaptability by exploiting diverse genetic resources. This study reports development and characterization of a set of inbred lines derived from a core germplasm collection of castor. The panel of 144 inbreds exhibited an excellent phenotypic diversity for morpho-agronomic traits related to plant architecture and yield components. However, SSR allelic diversity appears to be only moderate. The average number of alleles per SSR locus in the genotype panel was 3.0 and mean gene diversity was 0.38. Nevertheless, a majority of the inbred pairs (77 %) had very less estimated kinship coefficients (<0.05) suggesting that they were not related by pedigree. A very low level of genetic relatedness among the genotypes and absence of population structure suggest that this genotype panel consists of ideal set of materials for association mapping studies aiming at molecular breeding of key traits in castor. To our knowledge, this is the first report on the development and characterization of a large inbred collection representing the bulk of genetic diversity in castor, which can be further exploited for genetic, physiological and molecular studies towards achieving higher productivity.     

Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas putida S11

Here we report the genome sequence of a plant growth-promoting rhizobacterium, Pseudomonas putida S11. The length of the draft genome sequence is approximately 5,970,799 bp, with a G+C content of 62.4%. The genome contains 6,076 protein-coding sequences.     

Production of mycobacterial cell wall glycopeptidolipids requires a member of the MbtH-like protein family

ABSTRACT: BACKGROUND: Glycopeptidolipids (GPLs) are among the major free glycolipid components of the outer membrane of several saprophytic and clinically-relevant Mycobacterium species. The architecture of GPLs is based on a constant tripeptide-amino alcohol core of nonribosomal peptide synthetase origin that is N-acylated with a 3-hydroxy/methoxy acyl chain synthesized by a polyketide synthase and further decorated with variable glycosylation patterns built from methylated and acetylated sugars. GPLs have been implicated in many aspects of mycobacterial biology, thus highlighting the significance of gaining an understanding of their biosynthesis. Our bioinformatics analysis revealed that every GPL biosynthetic gene cluster known to date contains a gene (referred herein to as gplH) encoding a member of the MbtH-like protein family. Herein, we sought to conclusively establish whether gplH was required for GPL production. RESULTS: Deletion of gplH, a gene clustered with nonribosomal peptide synthetase-encoding genes in the GPL biosynthetic gene cluster of Mycobacterium smegmatis, produced a GPL deficient mutant. Transformation of this mutant with a plasmid expressing gplH restored GPL production. Complementation was also achieved by plasmid-based constitutive expression of mbtH, a paralog of gplH found in the biosynthetic gene cluster for production of the siderophore mycobactin of M. smegmatis. Further characterization of the gplH mutant indicated that it also displayed atypical colony morphology, lack of sliding motility, altered capacity for biofilm formation, and increased drug susceptibility. CONCLUSIONS: Herein, we provide evidence formally establishing that gplH is essential for GPL production in M. smegmatis. Inactivation of gplH also leads to a pleiotropic phenotype likely to arise from alterations in the cell envelope due to the lack of GPLs. While genes encoding MbtH-like proteins have been shown to be needed for production of siderophores and antibiotics, our study presents the first case of one such a gene proven to be required for production of a cell wall component. Furthermore, our results provide the first example of a mbtH-like gene with confirmed functional role in a member of the Mycobacterium genus. Altogether, our findings demonstrate a critical role of gplH in mycobacterial biology and advance our understanding of the genetic requirements for the biosynthesis of an important group of constituents of the mycobacterial outer membrane.