Guaranteeing a captive audience: coordinated regulation of gene transfer agent (GTA) production and recipient capability by cellular regulators

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Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery

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Inflammation neither increases hepatic hepcidin nor affects intestinal 59Fe-absorption in two murine models of bowel inflammation,hemizygous TNFΔARE/+ and homozygous IL-10−/− mice

Hepcidin-synthesis was reported to be stimulated by inflammation. In contrast, hepcidin synthesis was inhibited by TNFα and serum hepcidin was low. To elucidate these contradictions, we compare data on hepcidin expression, on iron absorption and homoeostasis and markers of inflammation between two murine models of intestinal inflammation and corresponding wild-types as determined by standard methods.In TNF^ΔARE/+ and IL-10^−/−-mice hepatic hepcidin expression and protein content was significantly lower than in corresponding wild-types. However, ⁵⁹Fe whole-body retention showed no difference between knock-outs and corresponding wild-types 7d after gavage, in neither strain. Compared to wild-types, body weight, hepatic non-haem iron content, hemoglobin and hematocrit were significantly decreased in TNF^ΔARE/+ mice, while erythropoiesis increased. These differences were not seen in IL-10^−/− mice. Duodenal IL-6 and TNFα content increased significantly in TNF^ΔARE/+ mice, while ferritin-H decreased along with hepatic hepcidin expression, ferritin L, and non-haem iron. In IL-10^−/− mice, these changes were less marked or missing for non-haem iron. Duodenal ferritin-L and ferroportin increased significantly, while HFE decreased.Our results corroborate the conflicting combination of low hepcidin with inflammation and without increased intestinal iron absorption. Speculating on underlying mechanism, decreased hepcidin may result from stimulated erythropoiesis. Unaltered intestinal iron-absorption may compromise between the stimulation by increased erythropoiesis and inhibition by local and systemic inflammation. The findings suggest intense interaction between counterproductive mechanisms and ask for further research.     

Novel clades of the HU/IHF superfamily point to unexpected roles in the eukaryotic centrosome,chromosome partitioning,and biologic conflicts

The HU superfamily of proteins, with a unique DNA-binding mode, has been extensively studied as the primary chromosome-packaging protein of the bacterial superkingdom. Representatives also play a role in DNA-structuring during recombination events and in eukaryotic organellar genome maintenance. However, beyond these well-studied roles, little is understood of the functional diversification of this large superfamily. Using sensitive sequence and structure analysis methods we identify multiple novel clades of the HU superfamily. We present evidence that a novel eukaryotic clade prototyped by the human CCDC81 protein acquired roles beyond DNA-binding, likely in protein-protein interaction in centrosome organization and as a potential cargo-binding protein in conjunction with Dynein-VII. We also show that these eukaryotic versions were acquired via an early lateral transfer from bacteroidetes, where we predict a role in chromosome partition. This likely happened before the last eukaryotic common ancestor, pointing to potential endosymbiont contributions beyond that of the mitochondrial progenitor. Further, we show that the dramatic lineage-specific expansion of this domain in the bacteroidetes lineage primarily is linked to a functional shift related to potential recognition and preemption of genome invasive entities such as mobile elements. Remarkably, the CCDC81 clade has undergone a similar massive lineage-specific expansion within the archosaurian lineage in birds, suggesting a possible use of the HU superfamily in a similar capacity in recognition of non-self molecules even in this case.     

A 3-hydroxy-3-methylglutaryl-CoA synthase-based probe for the discovery of the acyltransferase-less type I polyketide synthases

Acyltransferase (AT)-less type I polyketide synthases (PKSs) produce complex natural products due to the presence of many unique tailoring enzymes. The 3-hydroxy-3-methylglutaryl coenzyme A synthases (HCSs) are responsible for β-alkylation of the growing polyketide intermediates in AT-less type I PKSs. In this study, we discovered a large group of HCSs, closely associated with the characterized and orphan AT-less type I PKSs through in silico genome mining, sequence and genome neighbourhood network analyses. Using HCS-based probes, the survey of 1207 in-house strains and 18 soil samples from different geographic locations revealed the vast diversity of HCS-containing AT-less type I PKSs. The presence of HCSs in many AT-less type I PKSs suggests their co-evolutionary relationship. This study provides a new probe to study the abundance and diversity of AT-less type I PKSs in the environment and microbial strain collections. Our study should inspire future efforts to discover new polyketide natural products from AT-less type I PKSs.     

Sea ice detection from persistent single-channel shortwave infrared satellite data

The US Air Force has demonstrated an interest in deriving imagery products from classified military remote sensing platforms and making them available for civil and commercial operations. The US Air Force's Overhead Persistent Infrared (OPIR) is one such satellite constellation. A novel aspect of OPIR imagery is its near-continuous capture of single channel shortwave infrared data over the Arctic. Although traditionally used for missile warning and strategic defense, the exceptionally high temporal resolution of the OPIR data stream makes it an attractive source for Arctic remote sensing, particularly as the Arctic has warmed at a rate nearly double that of lower latitudes. This work assesses the feasibility of using Geostationary Operational Environmental Satellite – 16 (GOES-16) data as a proxy for OPIR imagery in the Arctic. Specifically, we seek to determine whether a single channel shortwave infrared (SWIR) approach can be used to detect and chart Arctic sea ice. We used a series of 32-image daily sets (4 images per hour x 8 h) over four-day periods acquired by GOES-16 in late April 2016 (as well as mid-March, mid-May, and mid-June) to chart sea ice, clouds and water in Hudson Bay, Canada. To do this, we applied image enhancement techniques to raw data imagery and then employed a time-based classification algorithm to the enhanced data cube. Overall, our method successfully discriminated sea ice from water and clouds when all conditions were present with improved discrimination over current daily products for sea ice charting in the Northern Hemisphere. The simple methodology of the developed algorithm is critical to ensuring the temporal resolution of the sensor is capitalized. The rapid timeline for production of this type of data is essential to the relevancy to military operations as well as emergency response/preparedness operations in the Arctic as it becomes more accessible in coming years. Our results make a compelling argument for the application of Air Force Missile Warning data to assist in the mapping, tracking, and assessment of sea ice in the high Arctic.     

Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae.

We report the potential phylogenetic utility of DNA sequence data from the last 700 bp of a ca. 1-kb intron of the MADS-box gene pistillata from a sampling of Sphaerocardamum species and other Brassicaceae. These results are compared with nrDNA ITS and the chloroplast trnL intron for the same taxa to demonstrate the potential phylogenetic utility of this pistillata intron and to identify potential historically independent sequences for an ongoing study of relationships within Sphaerocardamum. Analyses of the DNA sequence data for Brassicaceae indicated that pairwise divergences and potentially informative characters were higher in the pistillata intron (0.6-30.8%, 284 characters) and ITS (0-24%, 94 characters) than in the chloroplast trnL intron (0-4.2%, 17 characters). A comparison of Sphaerocardamum sequences identified low divergences and numbers of informative characters for trnL intron (0-2.4%, 1 character) and nrDNA ITS (0-2.5%, 2 characters) and substantially more variation among the pistillata sequences (0.15-3.7%, 19 characters). Phylogenetic analyses of these pistillata sequences fully resolve ingroup relationships without character conflict. Results of pistillata PCR amplifications from a broader dicot sample showed that some primers may be useful in amplifying orthologous pistillata sequences. Ultimately this pistillata intron may be a valuable source of phylogenetic characters at lower taxonomic levels.