Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to ...infrequently dividing or nondividing "persisters." Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although persistence in these studies was characterized by stable numbers of cells, this apparent stability was actually a dynamic state of balanced division and death. Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic pulses that were negatively correlated with cell survival. These behaviors may reflect epigenetic effects, because KatG pulsing and death were correlated between sibling cells. Selection of lineages characterized by infrequent KatG pulsing could allow nonresponsive adaptation during prolonged drug exposure.
The inverse care law states that disadvantaged populations need more health care than advantaged populations but receive less. Gaps in COVID-19-related health care and infection control are not well ...understood. We aimed to examine inequalities in health in the care cascade from testing for SARS-CoV-2 to COVID-19-related hospitalisation, intensive care unit (ICU) admission, and death in Switzerland, a wealthy country strongly affected by the pandemic.
We analysed surveillance data reported to the Swiss Federal Office of Public Health from March 1, 2020, to April 16, 2021, and 2018 population data. We geocoded residential addresses of notifications to identify the Swiss neighbourhood index of socioeconomic position (Swiss-SEP). The index describes 1·27 million small neighbourhoods of approximately 50 households each on the basis of rent per m2, education and occupation of household heads, and crowding. We used negative binomial regression models to calculate incidence rate ratios (IRRs) with 95% credible intervals (CrIs) of the association between ten groups of the Swiss-SEP index defined by deciles (1=lowest, 10=highest) and outcomes. Models were adjusted for sex, age, canton, and wave of the epidemic (before or after June 8, 2020). We used three different denominators: the general population, the number of tests, and the number of positive tests.
Analyses were based on 4 129 636 tests, 609 782 positive tests, 26 143 hospitalisations, 2432 ICU admissions, 9383 deaths, and 8 221 406 residents. Comparing the highest with the lowest Swiss-SEP group and using the general population as the denominator, more tests were done among people living in neighbourhoods of highest SEP compared with lowest SEP (adjusted IRR 1·18 95% CrI 1·02–1·36). Among tested people, test positivity was lower (0·75 0·69–0·81) in neighbourhoods of highest SEP than of lowest SEP. Among people testing positive, the adjusted IRR was 0·68 (0·62–0·74) for hospitalisation, was 0·54 (0·43–0·70) for ICU admission, and 0·86 (0·76–0·99) for death. The associations between neighbourhood SEP and outcomes were stronger in younger age groups and we found heterogeneity between areas.
The inverse care law and socioeconomic inequalities were evident in Switzerland during the COVID-19 epidemic. People living in neighbourhoods of low SEP were less likely to be tested but more likely to test positive, be admitted to hospital, or die, compared with those in areas of high SEP. It is essential to continue to monitor testing for SARS-CoV-2, access and uptake of COVID-19 vaccination and outcomes of COVID-19. Governments and health-care systems should address this pandemic of inequality by taking measures to reduce health inequalities in response to the SARS-CoV-2 pandemic.
Swiss Federal Office of Public Health, Swiss National Science Foundation, EU Horizon 2020, Branco Weiss Foundation.
End member mixing analysis (EMMA) is a commonly applied method to identify and quantify the dominant runoff producing sources of water. It employs tracers to determine the dimensionality of the ...hydrologic system. Many EMMA studies have been conducted using two to six tracers, with some of the main tracers being Ca, Na, Cl−, water isotopes, and alkalinity. Few studies use larger tracer sets including minor trace elements such as Li, Rb, Sr, and Ba. None of the studies has addressed the question of the tracer set size and composition, despite the fact that these determine which and how many end members (EM) will be identified. We examine how tracer set size and composition affects the conceptual model that results from an EMMA. We developed an automatic procedure that conducts EMMA while iteratively changing tracer set size and composition. We used a set of 14 tracers and 9 EMs. The validity of the resulting conceptual models was investigated under the aspects of dimensionality, EM combinations, and contributions to stream water. From the 16,369 possibilities, 23 delivered plausible results. The resulting conceptual models are highly sensitive to the tracer set size and composition. The moderate reproducibility of EM contributions indicates a still missing EM. It also emphasizes that the major elements are not always the most useful tracers and that larger tracer sets have an enhanced capacity to avoid false conclusions about catchment functioning. The presented approach produces results that may not be apparent from the traditional approach and it is a first step to add the idea of statistical significance to the EMMA approach.
Key Points
Resulting model of EMMA is highly sensitive to tracer set size and composition
Large tracer sets help to avoid false conclusions about runoff processes
Methodology to add statistical significance to the EMMA approach
Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA‐based processes via ...poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z‐nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate‐specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A.Z‐specificity and nucleosome interaction, whereas the PWWP domain exhibits direct DNA binding. Genome‐wide mapping reveals that PWWP2A binds selectively to H2A.Z‐containing nucleosomes with strong preference for promoters of highly transcribed genes. In human cells, its depletion affects gene expression and impairs proliferation via a mitotic delay. While PWWP2A does not influence H2A.Z occupancy, the C‐terminal tail of H2A.Z is one important mediator to recruit PWWP2A to chromatin. Knockdown of PWWP2A in Xenopus results in severe cranial facial defects, arising from neural crest cell differentiation and migration problems. Thus, PWWP2A is a novel H2A.Z‐specific multivalent chromatin binder providing a surprising link between H2A.Z, chromosome segregation, and organ development.
Synopsis
PWWP2A, a novel multivalent H2A.Z‐nucleosome binder, regulates mitotic progression in human cells and cranial facial morphogenesis during frog development, thereby providing a possible link between H2A.Z, chromosome segregation and organ development.
Histone H2A.Z interactome analyses identify PWWP2A as novel H2A.Z‐nucleosome binder.
Distinct regions in PWWP2A mediate nucleosome binding, H2A.Z specificity, and direct DNA interaction.
PWWP2A localizes to H2A.Z‐containing nucleosomes at transcriptional start sites of highly transcribed genes.
Depletion of PWWP2A in human cells results in changed gene expression profiles and severe mitotic defects without affecting H2A.Z occupancy.
PWWP2A loss during frog development affects proper neural crest stem cell differentiation and migration, causing severe cranial‐facial defects.
A novel histone variant‐specific interactor localizes to H2A.Z‐containing nucleosomes at start sites of highly transcribed genes, affecting gene expression profiles, cell division and organ development.
Immuno-oncology and cancer immunotherapies are areas of intense research. The numbers and locations of CD8+ tumor-infiltrating lymphocytes (TILs) are important measures of the immune response to ...cancer with prognostic, pharmacodynamic, and predictive potential. We describe the development, validation, and application of advanced image analysis methods to characterize multiple immunohistochemistry-derived CD8 parameters in clinical and nonclinical tumor tissues.
Commercial resection tumors from nine cancer types, and paired screening/on-drug biopsies of non-small-cell lung carcinoma (NSCLC) patients enrolled in a phase 1/2 clinical trial investigating the PD-L1 antibody therapy durvalumab (NCT01693562), were immunostained for CD8. Additional NCT01693562 samples were immunostained with a CD8/PD-L1 dual immunohistochemistry assay. Whole-slide scanning was performed, tumor regions were annotated by a pathologist, and images were analyzed with customized algorithms using Definiens Developer XD software. Validation of image analysis data used cell-by-cell comparison to pathologist scoring across a range of CD8+ TIL densities of all nine cancers, relying primarily on 95% confidence in having at least moderate agreement regarding Lin concordance correlation coefficient (CCC = 0.88-0.99, CCC_lower = 0.65-0.96).
We found substantial variability in CD8+ TILs between individual patients and across the nine types of human cancer. Diffuse large B-cell lymphoma had several-fold more CD8+ TILs than some other cancers. TIL densities were significantly higher in the invasive margin versus tumor center for carcinomas of head and neck, kidney and pancreas, and NSCLC; the reverse was true only for prostate cancer. In paired patient biopsies, there were significantly increased CD8+ TILs 6 weeks after onset of durvalumab therapy (mean of 365 cells/mm
over baseline; P = 0.009), consistent with immune activation. Image analysis accurately enumerated CD8+ TILs in PD-L1+ regions of lung tumors using the dual assay and also measured elongate CD8+ lymphocytes which constituted a fraction of overall TILs.
Validated image analysis accurately enumerates CD8+ TILs, permitting comparisons of CD8 parameters among tumor regions, individual patients, and cancer types. It also enables the more complex digital solutions needed to better understand cancer immunity, like analysis of multiplex immunohistochemistry and spatial evaluation of the various components comprising the tumor microenvironment.
ClinicalTrials.gov identifier: NCT01693562 . Study code: CD-ON-MEDI4736-1108. Interventional study (ongoing but not currently recruiting). Actual study start date: August 29, 2012. Primary completion date: June 23, 2017 (final data collection date for primary outcome measure).
The nucleus contains a plethora of different dynamic structures involved in the regulation and catalysis of nucleic acid metabolism and function. Over the past decades countless factors, molecular ...structures, interactions and posttranslational modifications have been described in this context. On the one side of the size scale X-ray crystallography delivers static snapshots of biomolecules at atomic resolution and on the other side light microscopy allows insights into complex structures of living cells and tissues in real time but poor resolution. Recent advances in light and electron microscopy are starting to close the temporal and spatial resolution gap from the atomic up to the cellular level. Old challenges and new insights are illustrated with examples of DNA replication and nuclear protein dynamics.
During the SARS-CoV-2 pandemic, many countries directed substantial resources toward genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort is ...necessary in national surveillance programs for SARS-CoV-2 and future pandemic threats. We aimed to investigate the effect of reduced sequencing on surveillance outcomes in a large genomic data set from Switzerland, comprising more than 143k sequences. We employed a uniform downsampling strategy using 100 iterations each to investigate the effects of fewer available sequences on the surveillance outcomes: (i) first detection of variants of concern (VOCs), (ii) speed of introduction of VOCs, (iii) diversity of lineages, (iv) first cluster detection of VOCs, (v) density of active clusters, and (vi) geographic spread of clusters. The impact of downsampling on VOC detection is disparate for the three VOC lineages, but many outcomes including introduction and cluster detection could be recapitulated even with only 35% of the original sequencing effort. The effect on the observed speed of introduction and first detection of clusters was more sensitive to reduced sequencing effort for some VOCs, in particular Omicron and Delta, respectively. A genomic surveillance program needs a balance between societal benefits and costs. While the overall national dynamics of the pandemic could be recapitulated by a reduced sequencing effort, the effect is strongly lineage-dependent-something that is unknown at the time of sequencing-and comes at the cost of accuracy, in particular for tracking the emergence of potential VOCs.IMPORTANCESwitzerland had one of the most comprehensive genomic surveillance systems during the COVID-19 pandemic. Such programs need to strike a balance between societal benefits and program costs. Our study aims to answer the question: How would surveillance outcomes have changed had we sequenced less? We find that some outcomes but also certain viral lineages are more affected than others by sequencing less. However, sequencing to around a third of the original effort still captured many important outcomes for the variants of concern such as their first detection but affected more strongly other measures like the detection of first transmission clusters for some lineages. Our work highlights the importance of setting predefined targets for a national genomic surveillance program based on which sequencing effort should be determined. Additionally, the use of a centralized surveillance platform facilitates aggregating data on a national level for rapid public health responses as well as post-analyses.
Oligonucleotides used in gene therapy and silencing are fragile compounds that degrade easily in biological environments. Porous biocompatible carrier particles may provide a useful strategy to ...deliver these therapeutics to their target sites. Development of appropriate delivery vehicles, however, requires a better understanding of the oligonucleotide‐host interactions and the oligonucleotide dynamics inside carrier particles. We investigated template‐free SBA‐15 type mesoporous silica particles and report their loading characteristics with siRNA depending on the surface functionalization of their porous network. We show that the siRNA uptake capability of the particles can be controlled by the composition of the functional groups. Fluorescence recovery after photobleaching measurements revealed size‐dependent mobility of siRNA and double‐stranded DNA oligonucleotides within the functionalized silica particles and provided evidence for the stability of the oligonucleotides inside the pores. Hence, our study demonstrates the potential of mesoporous silica particles as a means for alternative gene delivery in nanomedicine.
Template‐free SBA‐15 type mesoporous silica particles are loaded with siRNA and dsDNA. The particles’ uptake capability is controlled by an organic surface functionalization and the dynamics of the intact oligonucleotides inside the functionalized nanochannels determined. The study demonstrates the potential of mesoporous silica as an alternative means for gene delivery. Such alternatives are urgently needed since the delivery of oligonucleotides to their target sites still represents a major hurdle in the application of gene therapy.
Private gardens make up large parts of urban green space. In contrast to public green spaces, planning and management is usually uncoordinated and independent of municipal planning and management ...strategies. Therefore, the potential for private gardens to provide ecosystem services and habitat and to function as corridors for wildlife is not fully utilized. In order to improve public knowledge on gardens, as well as provide individual gardeners with information on what they can contribute to enhance ecosystem services provision, we developed a GIS-based web application for the city of Braunschweig (Germany): the ‘GartenApp’ (garden app). Users of the app have to outline their garden on a web map and provide information on biodiversity related features and management practices. Finally, they are asked about observations of well recognizable species in their gardens. As an output, the gardeners are provided with an estimate of the ecosystem services their garden provides, with an evaluation of the biodiversity friendliness, customized advice on improving ecosystem services provision, and results from connectivity models that show gardeners the role of their garden in the green network of the city. In this paper, we describe the app architecture and show the first results from its application. We finish with a discussion on the potential of GIS-based web applications for urban sustainability, planning and conservation.
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