Single Cell Cryo-Soft X-ray Tomography Shows That Each Chlamydia Trachomatis Inclusion Is a Unique Community of Bacteria

Chlamydiae are strict intracellular pathogens residing within a specialised membrane-bound compartment called the inclusion. Therefore, each infected cell can, be considered as a single entity where bacteria form a community within the inclusion. It remains unclear as to how the population of bacteria within the inclusion influences individual bacterium. The life cycle of Chlamydia involves transitioning between the invasive elementary bodies (EBs) and replicative reticulate bodies (RBs). We have used cryo-soft X-ray tomography to observe individual inclusions, an approach that combines 40 nm spatial resolution and large volume imaging (up to 16 µm). Using semi-automated segmentation pipeline, we considered each inclusion as an individual bacterial niche. Within each inclusion, we identifyed and classified different forms of the bacteria and confirmed the recent finding that RBs have a variety of volumes (small, large and abnormal). We demonstrate that the proportions of these different RB forms depend on the bacterial concentration in the inclusion. We conclude that each inclusion operates as an autonomous community that influences the characteristics of individual bacteria within the inclusion

Estimating survival in patients with gastrointestinal cancers and brain metastases: An update of the graded prognostic assessment for gastrointestinal cancers (GI-GPA).

BackgroundPatients with gastrointestinal cancers and brain metastases (BM) represent a unique and heterogeneous population. Our group previously published the Diagnosis-Specific Graded Prognostic Assessment (DS-GPA) for patients with GI cancers (GI-GPA) (1985-2007, n = 209). The purpose of this study is to update the GI-GPA based on a larger contemporary database.MethodsAn IRB-approved consortium database analysis was performed using a multi-institutional (18), multi-national (3) cohort of 792 patients with gastrointestinal (GI) cancers, with newly-diagnosed BM diagnosed between 1/1/2006 and 12/31/2017. Survival was measured from date of first treatment for BM. Multiple Cox regression was used to select and weight prognostic factors in proportion to their hazard ratios. These factors were incorporated into the updated GI-GPA.ResultsMedian survival (MS) varied widely by primary site and other prognostic factors. Four significant factors (KPS, age, extracranial metastases and number of BM) were used to formulate the updated GI-GPA. Overall MS for this cohort remains poor; 8 months. MS by GPA was 3, 7, 11 and 17 months for GPA 0-1, 1.5-2, 2.5-3.0 and 3.5-4.0, respectively. >30% present in the worst prognostic group (GI-GPA of ≤1.0).ConclusionsBrain metastases are not uncommon in GI cancer patients and MS varies widely among them. This updated GI-GPA index improves our ability to estimate survival for these patients and will be useful for therapy selection, end-of-life decision-making and stratification for future clinical trials. A user-friendly, free, on-line app to calculate the GPA score and estimate survival for an individual patient is available at brainmetgpa.com

Interaction of RNA polymerase II and the small RNA machinery affects heterochromatic silencing in Drosophila

<p>Abstract</p> <p>Background</p> <p>Heterochromatin is the tightly packaged dynamic region of the eukaryotic chromosome that plays a vital role in cellular processes such as mitosis and meiotic recombination. Recent experiments in <it>Schizosaccharomyces pombe </it>have revealed the structure of centromeric heterochromatin is affected in RNAi pathway mutants. It has also been shown in fission yeast that the heterochromatin barrier is traversed by RNA Pol II and that the passage of RNA Pol II through heterochromatin is important for heterochromatin structure. Thus, an intricate interaction between the RNAi machinery and RNA Pol II affects heterochromatin structure. However, the role of the RNAi machinery and RNA Pol II on the metazoan heterochromatin landscape is not known. This study analyses the interaction of the small RNA machinery and RNA Pol II on <it>Drosophila </it>heterochromatin structure.</p> <p>Results</p> <p>The results in this paper show genetic and biochemical interaction between RNA Pol II (largest and second largest subunit) and small RNA silencing machinery components (<it>dcr-2, ago1, ago2, piwi, Lip [D], aub </it>and <it>hls</it>). Immunofluorescence analysis of polytene chromosomes from trans-heterozygotes of RNA Pol II and different mutations of the small RNA pathways show decreased H3K9me2 and mislocalization of Heterochromatin protein-1. A genetic analysis performed on these mutants showed a strong suppression of <it>white-mottled4h </it>position effect variegation. This was further corroborated by a western blot analysis and chromatin immunoprecipitation, which showed decreased H3K9me2 in trans-heterozygote mutants compared to wild type or single heterozygotes. Co-immunoprecipitation performed using <it>Drosophila </it>embryo extracts showed the RNA Pol II largest subunit interacting with Dcr-2 and dAGO1. Co-localization performed on polytene chromosomes showed RNA Pol II and dAGO1 overlapping at some sites.</p> <p>Conclusion</p> <p>Our experiments show a genetic and biochemical interaction between RNA Pol II (largest and second largest subunits) and the small RNA silencing machinery in <it>Drosophila</it>. The interaction has functional aspects in terms of determining H3K9me2 and HP-1 deposition at the chromocentric heterochromatin. Thus, RNA Pol II has an important role in establishing heterochromatin structure in <it>Drosophila</it>.</p

March 1955

Presidents Report - Frank P. Dunlap (page 1) The Student Purdue Serves - Dr. N. M. Parkhurst (2) A Student Reports - Bill Roach (4) Corrective Management of Shrubs - H. W. Gilbert (5) Nutrient Absorption by Plants - J. R. Watson Jr. (7) Disease Development is Slow - Dr. Wm. Klomparens (10) Poa Annua Control with Arsenic Materials - W. H. Daniel (11) Labor Relations - Cincinnati Country Club - John McCoy (14) Labor Policies at my Course - Ernest Schneider (15) Labor Policies at my Course - Don Strand (16) Nitrogen Use and Why - Robert M. Williams (17) Fertilizing Greens and Why - Don Likes(18) Nitrogen Use and Why - Lawrence Huber (20) Report on Experimental Green - Taylor Boyd (21) Experiences with Fairway Improvements - Ray Davis (23) Fairway Improvement Program - Bert Rost (24) Experiences on Merion Bluegrass - Carl Habenicht (24) Merion Bluegrass Experiences - P. E. Drachman (25) Zoysia for Lawns and Nurseries - P. E. Drachman (27) Preparation for Mortorized Carts - James W. Brandt (28) Preparing for Motorized Carts - Carl Bretzlaff (29) Merion Bluegrass Experiences - Ben O. Warren (31) Pennlu Distribution - W. H. Daniel(32) Zoysia for Midwest Lawns - W. H. Daniel (34) Crabgrass Prevention and Control - W. H. Daniel (36) Plant Carbohydrates Must Balance Nitrogen - M. R. Teel (39) Put Yourself in His Place - Fred Grau (40) Nitrogen Use and Why Wm. E. Lyons (45) The Management of Bentgrass Fairways - O. J. Noer (49) Fairway Improvement Program O. W. Young (52) Experiences with Zoysia - Ferank Dinelli (53

Biologically induced mineralization of dypingite by cyanobacteria from an alkaline wetland near Atlin, British Columbia, Canada

Background: This study provides experimental evidence for biologically induced precipitation of magnesium carbonates, specifically dypingite (Mg(CO)(OH) ·5HO), by cyanobacteria from an alkaline wetland near Atlin, British Columbia. This wetland is part of a larger hydromagnesite (Mg(CO)(OH) ·4HO) playa. Abiotic and biotic processes for magnesium carbonate precipitation in this environment are compared. Results: Field observations show that evaporation of wetland water produces carbonate films of nesquehonite (MgCO ·3HO) on the water surface and crusts on exposed surfaces. In contrast, benthic microbial mats possessing filamentous cyanobacteria (Lyngbya sp.) contain platy dypingite (Mg (CO)4(OH)·5HO) and aragonite. Bulk carbonates in the benthic mats (δC avg. = 6.7%, δO avg. = 17.2%) were isotopically distinguishable from abiotically formed nesquehonite (δC avg. = 9.3%, δO avg. = 24.9%). Field and laboratory experiments, which emulated natural conditions, were conducted to provide insight into the processes for magnesium carbonate precipitation in this environment. Field microcosm experiments included an abiotic control and two microbial systems, one containing ambient wetland water and one amended with nutrients to simulate eutrophic conditions. The abiotic control developed an extensive crust of nesquehonite on its bottom surface during which [Mg] decreased by 16.7% relative to the starting concentration. In the microbial systems, precipitation occurred within the mats and was not simply due to the capturing of mineral grains settling out of the water column. Magnesium concentrations decreased by 22.2% and 38.7% in the microbial systems, respectively. Laboratory experiments using natural waters from the Atlin site produced rosettes and flakey globular aggregates of dypingite precipitated in association with filamentous cyanobacteria dominated biofilms cultured from the site, whereas the abiotic control again precipitated nesquehonite. Conclusion: Microbial mats in the Atlin wetland create ideal conditions for biologically induced precipitation of dypingite and have presumably played a significant role in the development of this natural Mg-carbonate playa. This biogeochemical process represents an important link between the biosphere and the inorganic carbon pool

Coordination of microtubule and microfilament dynamics by Drosophila Rho1, Spire, and Cappuccino

The actin nucleation factors Spire and Cappuccino regulate the onset of ooplasmic streaming in Drosophila1-5. Although this streaming event is microtubule-based, actin assembly is required for its timing. It is not understood how the interaction of microtubules and microfilaments is mediated in this context. Here we demonstrate that Cappuccino and Spire have microtubule and microfilament crosslinking activity. The spire locus encodes several distinct protein isoforms (SpireA, SpireC, and SpireD). SpireD was recently shown to nucleate actin, but the activity of the other isoforms has not been addressed. We find that SpireD does not have crosslinking activity, while SpireC is a potent crosslinker. We show that SpireD binds to Cappuccino and inhibits Factin/ microtubule crosslinking, and activated Rho1 abolishes this inhibition, establishing a mechanistic basis for the regulation of Capu and Spire activity. We propose that Rho1, cappuccino and spire are elements of a conserved developmental cassette that is capable of directly mediating crosstalk between microtubules and microfilaments

An Image Statistics–Based Model for Fixation Prediction

The problem of predicting where people look at, or equivalently salient region detection, has been related to the statistics of several types of low-level image features. Among these features, contrast and edge information seem to have the highest correlation with the fixation locations. The contrast distribution of natural images can be adequately characterized using a two-parameter Weibull distribution. This distribution catches the structure of local contrast and edge frequency in a highly meaningful way. We exploit these observations and investigate whether the parameters of the Weibull distribution constitute a simple model for predicting where people fixate when viewing natural images. Using a set of images with associated eye movements, we assess the joint distribution of the Weibull parameters at fixated and non-fixated regions. Then, we build a simple classifier based on the log-likelihood ratio between these two joint distributions. Our results show that as few as two values per image region are already enough to achieve a performance comparable with the state-of-the-art in bottom-up saliency prediction