Transposon insertion mapping with PIMMS, Pragmatic Insertional Mutation Mapping System

The PIMMS (Pragmatic Insertional Mutation Mapping System) pipeline has beendeveloped for simple conditionally essential genome discovery experiments in bacteria.Capable of using raw sequence data files alongside a FASTA sequence of thereference genome and GFF file, PIMMS will generate a tabulated output of each codingsequence with corresponding mapped insertions accompanied with normalized resultsenabling streamlined analysis. This allows for a quick assay of the genome to identifyconditionally essential genes on a standar d desktop computer prioritizing results forfurther investigation

Carcinosarcoma of the breast: two case reports and review of the literature

Carcinosarcoma of the breast, often referred to as metaplastic carcinoma of the breast, is a rare malignancy with two distinct cell lines described as a breast carcinoma of ductal type with a sarcoma-like component. Clinically, carcinosarcoma of the breast is an aggressive breast cancer. The prognosis for carcinosarcoma of the breast is less favorable compared to more common types of breast cancer such as infiltrating ductal or lobular carcinoma. Currently, the evaluation of breast carcinoma includes hormone receptor analysis of the tumor tissue, with those positive for estrogen or progesterone responding better to both hormonal and chemotherapy

Complete genome sequence of Streptococcus agalactiae strain 01173, isolated from Kuwaiti wild fish

© 2020 Santi et al. Here, we report the complete genome of piscine Streptococcus agalactiae 01173 serotype Ia, which was generated using long-read sequencing technology. The bacteria were isolated from wild fish displaying signs of streptococcosis, from a fish kill incident in Kuwait

N-representability and stationarity in time-dependent density functional theory

To construct an N-representable time-dependent density-functional theory, a generalization to the time domain of the Levy-Lieb (LL) constrained search algorithm is required. That the action is only stationary in the Dirac-Frenkel variational principle eliminates the possibility of basing the search on the action itself. Instead, we use the norm of the partial functional derivative of the action in the Hilbert space of the wave functions in place of the energy of the LL search. The electron densities entering the formalism are $N$-representable, and the resulting universal action functional has a unique stationary point in the density at that corresponding to the solution of the Schr\"{o}dinger equation. The original Runge-Gross (RG) formulation is subsumed within the new formalism. Concerns in the literature about the meaning of the functional derivatives and the internal consistency of the RG formulation are allayed by clarifying the nature of the functional derivatives entering the formalism.Comment: 9 pages, 0 figures, Phys. Rev. A accepted. Introduction was expanded, subsections reorganized, appendix and new references adde

PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data

MotivationCurrent methods for visualising and interrogating high-throughput transposon insertion mutagenesis sequencing (TIS) data requires a significant time investment in learning bioinformatics, often producing static figures that do not facilitate real time analysis.SummaryWe have created an accessible web-based browser tool for visualisation and downstream analysis of high-throughput TIS data results generated by the PIMMS analysis pipeline. This includes multiple interactive and sortable tables to aid the user to identify genes of interest, enabling the user to gain a greater understanding of the genes contributing to fitness in their experimental work. PIMMS-Dash permits researchers, with any level of bioinformatics knowledge, to interrogate data sets and generate publication quality figures.AvailabilityPIMMS-Dash is freely available and is accessible online at https://pimms-dashboard-uon.azurewebsites.net and a Docker containerised version is available at https://github.com/Streptococcal-Research-Group/PIMMS-Dash to run locally

Multi-Attribute Tradespace Exploration for Survivability

Multi-Attribute Tradespace Exploration for Survivability is a system design and analysis methodology that incorporates survivability considerations into the tradespace exploration process (i.e., a solution-generating and decision-making framework that applies decision theory to model-based design). During the concept generation phase of tradespace exploration, the methodology applies seventeen empirically validated survivability design principles spanning susceptibility reduction, vulnerability reduction, and resilience enhancement. During subsequent concept evaluation, the methodology adds value-based survivability metrics to traditional architectural evaluation criteria of mission utility and lifecycle cost. Applied to a satellite radar mission, the methodology allowed operational survivability to be statistically evaluated across representative distributions of naturally occurring disturbances in the space environment and for survivability to be incorporated as a decision factor earlier in the design process. Constellations in the illustrative example are shown to be the most survivable, mitigating disturbances architecturally, rather than through additive features.Massachusetts Institute of Technology (Systems Engineering Advancement Research Initiative (SEAri))Massachusetts Institute of Technology. Program on Emerging Technologie

Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome

© 2020, © 2020 The Author(s). Published with license by Taylor & Francis Group, LLC. Background: The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants. Results: We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3rd generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism. Conclusions: We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations

A paradox in bacterial pathogenesis: Activation of the local macrophage inflammasome is required for virulence of streptococcus uberis

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Streptococcus uberis is a common cause of intramammary infection and mastitis in dairy cattle. Unlike other mammary pathogens, S. uberis evades detection by mammary epithelial cells, and the host–pathogen interactions during early colonisation are poorly understood. Intramammary challenge of dairy cows with S. uberis (strain 0140J) or isogenic mutants lacking the surface-anchored serine protease, SUB1154, demonstrated that virulence was dependent on the presence and correct location of this protein. Unlike the wild-type strain, the mutant lacking SUB1154 failed to elicit IL-1β from ex vivo CD14+ cells obtained from milk (bovine mammary macrophages, BMM), but this response was reinstated by complementation with recombinant SUB1154; the protein in isolation elicited no response. Production of IL-1β was ablated in the presence of various inhibitors, indicating dependency on internalisation and activation of NLRP3 and caspase-1, consistent with inflammasome activation. Similar transcriptomic changes were detected in ex vivo BMM in response to the wild-type or the SUB1154 deletion mutant, consistent with S. uberis priming BMM, enabling the SUB1154 protein to activate inflammasome maturation in a transcriptionally independent manner. These data can be reconciled in a novel model of pathogenesis in which, paradoxically, early colonisation is dependent on the innate response to the initial infection