Genome sequencing and annotation of Acinetobacter gyllenbergii strain MTCC 11365T

AbstractThe genus Acinetobacter consists of 31 validly published species ubiquitously distributed in nature and primarily associated with nosocomial infection. We report 4.3Mb genome of the Acinetobacter gyllenbergii strain MTCC 11365T. The draft genome of A. gyllenbergii has a G+C content of 41.0% and includes 3 rRNA genes (5S, 23S, 16S) and 67 aminoacyl-tRNA synthetase genes

Genome sequencing and annotation of Acinetobacter guillouiae strain MSP 4-18

AbstractThe genus Acinetobacter consists of 31 validly published species ubiquitously distributed in nature and primarily associated with nosocomial infection. We report the 4.8Mb genome of Acinetobacter guillouiae MSP 4-18, isolated from a mangrove soil sample from Parangipettai (11°30′N, 79°47′E), Tamil Nadu, India. The draft genome of A. guillouiae MSP 4-18 has a G+C content of 38.0% and includes 3 rRNA genes (5S, 23S, 16S) and 69 aminoacyl-tRNA synthetase genes

Evidence of a new metabolic capacity in an emerging diarrheal pathogen: lessons from the draft genomes of Vibrio fluvialis strains PG41 and I21563

BACKGROUND: Vibrio fluvialis is an emerging diarrheal pathogen for which no genome is currently available. In this work, draft genomes of two closely related clinical strains PG41 and I21563 have been explored. RESULTS: V. fluvialis strains PG41 and I21563 were sequenced on the Illumina HiSeq 1000 platform to obtain draft genomes of 5.3 Mbp and 4.4 Mbp respectively. Our genome data reveal the presence of genes involved in ethanolamine utilization, which is further experimentally confirmed by growth analysis. CONCLUSIONS: Combined in silico and growth analysis establish a new metabolic capacity of V. fluvialis to harvest energy from ethanolamine

Ablation of RNA interference and retrotransposons accompany acquisition and evolution of transposases to heterochromatin protein CENPB

Inactivation of retrotransposons is accompanied by the emergence of centromere-binding protein-B (CENPB) in Schizosaccharomyces, as well as in metazoans. The RNA interference (RNAi)-induced transcriptional silencing (RITS) complex, comprising chromodomain protein-1 (Chp1), Tas3 (protein with unknown function), and Argonaute (Ago1), plays an important role in RNAi-mediated heterochromatinization. We find that whereas the Ago1 subunit of the RITS complex is highly conserved, Tas3 is lost and Chp1 is truncated in Schizosaccharomyces cryophilus and Schizosaccharomyces octosporus. We show that truncated Chp1 loses the property of heterochromatin localization and silencing when transformed in Schizosaccharomyces pombe. Furthermore, multiple copies of CENPB, related to Tc1/mariner and Tc5 transposons, occur in all Schizosaccharomyces species, as well as in humans, but with loss of transposase function (except Schizosaccharomyces japonicus). We propose that acquisition of Tc1/mariner and Tc5 elements by horizontal transfer in S. pombe (and humans) is accompanied by alteration of their function from a transposase/endonuclease to a heterochromatin protein, designed to suppress transposon expression and recombination. The resulting redundancy of RITS may have eased the selection pressure, resulting in progressive loss or truncation of tas3 and chp1 genes in S. octosporus and S. cryophilus and triggered similar evolutionary dynamics in the metazoan orthologues

Highly Sensitive Flow Cytometry Allows Monitoring of Changes in Circulating Immune Cells in Blood After Tdap Booster Vaccination

© 2021 Diks, Khatri, Oosten, de Mooij, Groenland, Teodosio, Perez-Andres, Orfao, Berbers, Zwaginga, van Dongen and Berkowska.Antigen-specific serum immunoglobulin (Ag-specific Ig) levels are broadly used as correlates of protection. However, in several disease and vaccination models these fail to predict immunity. In these models, in-depth knowledge of cellular processes associated with protective versus poor responses may bring added value. We applied high-throughput multicolor flow cytometry to track over-time changes in circulating immune cells in 10 individuals following pertussis booster vaccination (Tdap, Boostrix®, GlaxoSmithKline). Next, we applied correlation network analysis to extensively investigate how changes in individual cell populations correlate with each other and with Ag-specific Ig levels. We further determined the most informative cell subsets and analysis time points for future studies. Expansion and maturation of total IgG1 plasma cells, which peaked at day 7 post-vaccination, was the most prominent cellular change. Although these cells preceded the increase in Ag-specific serum Ig levels, they did not correlate with the increase of Ig levels. In contrast, strong correlation was observed between Ag-specific IgGs and maximum expansion of total IgG1 and IgA1 memory B cells at days 7 to 28. Changes in circulating T cells were limited, implying the need for a more sensitive approach. Early changes in innate immune cells, i.e. expansion of neutrophils, and expansion and maturation of monocytes up to day 5, most likely reflected their responses to local damage and adjuvant. Here we show that simultaneous monitoring of multiple circulating immune subsets in blood by flow cytometry is feasible. B cells seem to be the best candidates for vaccine monitoring.K is supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 707404. The here presented study is a pilot study for the Innovative Medicines Initiative (IMI) PERISCOPE program, a Joint Undertaking under grant agreement No 115910. This Joint Undertaking receives support from the European Union’s Horizon 2020 Research and Innovation Programme, the European Federation of Pharmaceutical Industries and Associations (EFPIA), and the Bill and Melinda Gates Foundation (BMGF). The flow cytometric studies in this study were supported by the EuroFlow Consortium. The EuroFlow Consortium received support from the FP6-2004-LIFESCIHEALTH-5 program of the European Commission (grant LSHB-CT-2006-018708) as Specific Targeted Research Project (STREP)

DataSheet_1_Development of a standardized and validated flow cytometry approach for monitoring of innate myeloid immune cells in human blood.zip

Innate myeloid cell (IMC) populations form an essential part of innate immunity. Flow cytometric (FCM) monitoring of IMCs in peripheral blood (PB) has great clinical potential for disease monitoring due to their role in maintenance of tissue homeostasis and ability to sense micro-environmental changes, such as inflammatory processes and tissue damage. However, the lack of standardized and validated approaches has hampered broad clinical implementation. For accurate identification and separation of IMC populations, 62 antibodies against 44 different proteins were evaluated. In multiple rounds of EuroFlow-based design-testing-evaluation-redesign, finally 16 antibodies were selected for their non-redundancy and separation power. Accordingly, two antibody combinations were designed for fast, sensitive, and reproducible FCM monitoring of IMC populations in PB in clinical settings (11-color; 13 antibodies) and translational research (14-color; 16 antibodies). Performance of pre-analytical and analytical variables among different instruments, together with optimized post-analytical data analysis and reference values were assessed. Overall, 265 blood samples were used for design and validation of the antibody combinations and in vitro functional assays, as well as for assessing the impact of sample preparation procedures and conditions. The two (11- and 14-color) antibody combinations allowed for robust and sensitive detection of 19 and 23 IMC populations, respectively. Highly reproducible identification and enumeration of IMC populations was achieved, independently of anticoagulant, type of FCM instrument and center, particularly when database/software-guided automated (vs. manual “expert-based”) gating was used. Whereas no significant changes were observed in identification of IMC populations for up to 24h delayed sample processing, a significant impact was observed in their absolute counts after >12h delay. Therefore, accurate identification and quantitation of IMC populations requires sample processing on the same day. Significantly different counts were observed in PB for multiple IMC populations according to age and sex. Consequently, PB samples from 116 healthy donors (8-69 years) were used for collecting age and sex related reference values for all IMC populations. In summary, the two antibody combinations and FCM approach allow for rapid, standardized, automated and reproducible identification of 19 and 23 IMC populations in PB, suited for monitoring of innate immune responses in clinical and translational research settings.Peer reviewe

Theoretical analysis of excitation energies and transition parameters of C-like ions

Relativistic configuration interaction results are presented for several C-like ions (Kr XXXI, Rb XXXII, Sr XXXIII) using the multi-configuration Dirac–Hartree–Fock (MCDHF) method. The calculations are performed in the active space approximation with the inclusion of the Breit interaction, the finite nuclear size effect and quantum electrodynamic corrections. Results for fine structure energy levels for 2s22p2, 2s2p3 and 2p4 configurations relative to the ground state are reported. The transition wavelengths, transition probabilities, line strengths and absorption oscillator strengths for electric dipole (E1) and magnetic quadrupole (M2) transitions are calculated among first 20 levels. The core-valence correlation effects are taken into account through single-double multireference expansions to increasing sets of active orbitals up to n = 7. Our calculated results are found to be very close to other available theoretical and experimental values. We hope that our results will be useful for experimentalists in identifying the fine structure levels in the future

Ethanolamine utilization in <it>Vibrio alginolyticus</it>

<p>Abstract</p> <p>Ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the <it>eut</it>-operon. Previous studies have revealed the presence of <it>eutBC</it> genes encoding ethanolamine-ammonia lyase, a key enzyme that breaks ethanolamine into acetaldehyde and ammonia, in about 100 bacterial genomes including members of gamma-proteobacteria. However, ethanolamine utilization has not been reported for any member of the <it>Vibrio</it> genus. Our comparative genomics study reveals the presence of genes that are involved in ethanolamine utilization in several <it>Vibrio</it> species. Using <it>Vibrio alginolyticus</it> as a model system we demonstrate that ethanolamine is better utilized as a nitrogen source than as a carbon source.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Lakshminarayan Iyer and Dr. Vivek Anantharaman (nominated by Dr. L Aravind).</p