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Assays to accurately estimate relative fitness of bacteria growing in multistrain communities can advance our understanding of how selection shapes diversity within a lineage. Here, we present a variant of the “evolve and resequence” approach both to estimate relative fitness and to identify genetic variants responsible for fitness variation of symbiotic bacteria in free-living and host environments. We demonstrate the utility of this approach by characterizing selection by two plant hosts and in two free-living environments (sterilized soil and liquid media) acting on synthetic communities of the facultatively symbiotic bacterium Ensifer meliloti. We find (i) selection that hosts exert on rhizobial communities depends on competition among strains, (ii) selection is stronger inside hosts than in either free-living environment, and (iii) a positive host-dependent relationship between relative strain fitness in multistrain communities and host benefits provided by strains in single-strain experiments. The greatest changes in allele frequencies in response to plant hosts are in genes associated with motility, regulation of nitrogen fixation, and host/rhizobia signaling. The approach we present provides a powerful complement to experimental evolution and forward genetic screens for characterizing selection in bacterial populations, identifying gene function, and surveying the functional importance of naturally occurring genomic variation.

Historical change in the availability of kin beyond the household has long interested scholars, but there has been little comparable evidence on long-run change. While generally accepted that individuals lived near kin historically, no systematic measures have been available to assess historical kin propinquity at the national level. With the release of historical complete count United States census data from the Integrated Public Use Microdata Series (IPUMS), a robust estimate of patrilineal kin propinquity for the United States nationally from 1790 to 1940 is calculated. Defined as the probability of non-random isonymy within an enumeration district, the estimate of patrilineal kin propinquity relies on the sequential ordering of households in the census. The United States experienced a long-run decline in patrilineal kin propinquity from nearly 50% of households in 1790 to 17% of households in 1940. The age patterns of kin propinquity show substantial variation across the life course, and regional differences demonstrate the impact of economic and demographic conditions. The decline in kin propinquity reflected urbanization and the decline of agriculture, declining kin availability, growing distance between potential kin links, and a change in preferences of living near kin. This is the first study to produce a systematic estimate of patrilineal kin propinquity at the national level for the United States between 1790 and 1940. Researchers can use this meaningful measure of patrilineal kin propinquity to better explain its relationships with other demographic behaviors and outcomes such as fertility, mortality, and migration choices.

CD47, a \"don't eat me\" signal for phagocytic cells, is expressed on the surface of all human solid tumor cells. Analysis of patient tumor and matched adjacent normal (nontumor) tissue revealed that CD47 is overexpressed on cancer cells. CD47 mRNA expression levels correlated with a decreased probability of survival for multiple types of cancer. CD47 is a ligand for SIRPα, a protein expressed on macrophages and dendritic cells. In vitro, blockade of CD47 signaling using targeted monoclonal antibodies enabled macrophage phagocytosis of tumor cells that were otherwise protected. Administration of anti-CD47 antibodies inhibited tumor growth in orthotopic immunodeficient mouse xenotransplantation models established with patient tumor cells and increased the survival of the mice over time. Anti-CD47 antibody therapy initiated on larger tumors inhibited tumor growth and prevented or treated metastasis, but initiation of the therapy on smaller tumors was potentially curative. The safety and efficacy of targeting CD47 was further tested and validated in immune competent hosts using an orthotopic mouse breast cancer model. These results suggest all human solid tumor cells require CD47 expression to suppress phagocytic innate immune surveillance and elimination. These data, taken together with similar findings with other human neoplasms, show that CD47 is a commonly expressed molecule on all cancers, its function to block phagocytosis is known, and blockade of its function leads to tumor cell phagocytosis and elimination. CD47 is therefore a validated target for cancer therapies.

Rett syndrome (RTT) is a severe X-linked neurodevelopmental disorder mainly affecting females and is associated with mutations in MECP2, the gene encoding methyl CpG-binding protein 2. Mouse models suggest that recombinant human insulin-like growth factor 1 (IGF-1) (rhIGF1) (mecasermin) may improve many clinical features. We evaluated the safety, tolerability, and pharmacokinetic profiles of IGF-1 in 12 girls with MECP2 mutations (9 with RTT). In addition, we performed a preliminary assessment of efficacy using automated cardiorespiratory measures, EEG, a set of RTT-oriented clinical assessments, and two standardized behavioral questionnaires. This phase 1 trial included a 4-wk multiple ascending dose (MAD) (40—120 μg/kg twice daily) period and a 20-wk open-label extension (OLE) at the maximum dose. Twelve subjects completed the MAD and 10 the entire study, without evidence of hypoglycemia or serious adverse events. Mecasermin reached the CNS compartment as evidenced by the increase in cerebrospinal fluid IGF-1 levels at the end of the MAD. The drug followed nonlinear kinetics, with greater distribution in the peripheral compartment. Cardiorespiratory measures showed that apnea improved during the OLE. Some neurobehavioral parameters, specifically measures of anxiety and mood also improved during the OLE. These improvements in mood and anxiety scores were supported by reversal of right frontal alpha band asymmetry on EEG, an index of anxiety and depression. Our data indicate that IGF-1 is safe and well tolerated in girls with RTT and, as demonstrated in preclinical studies, ameliorates certain breathing and behavioral abnormalities.

Tandem repeat (TR) variation is associated with gene expression changes and numerous rare monogenic diseases. Although long-read sequencing provides accurate full-length sequences and methylation of TRs, there is still a need for computational methods to profile TRs across the genome. Here we introduce the Tandem Repeat Genotyping Tool (TRGT) and an accompanying TR database. TRGT determines the consensus sequences and methylation levels of specified TRs from PacBio HiFi sequencing data. It also reports reads that support each repeat allele. These reads can be subsequently visualized with a companion TR visualization tool. Assessing 937,122 TRs, TRGT showed a Mendelian concordance of 98.38%, allowing a single repeat unit difference. In six samples with known repeat expansions, TRGT detected all expansions while also identifying methylation signals and mosaicism and providing finer repeat length resolution than existing methods. Additionally, we released a database with allele sequences and methylation levels for 937,122 TRs across 100 genomes. A set of tools maps tandem repeats across complete genomes.

Proteomic profiling of brain cell types using isolation-based strategies pose limitations in resolving cellular phenotypes representative of their native state. We describe a mouse line for cell type-specific expression of biotin ligase TurboID, for in vivo biotinylation of proteins. Using adenoviral and transgenic approaches to label neurons, we show robust protein biotinylation in neuronal soma and axons throughout the brain, allowing quantitation of over 2000 neuron-derived proteins spanning synaptic proteins, transporters, ion channels and disease-relevant druggable targets. Next, we contrast Camk2a-neuron and Aldh1l1-astrocyte proteomes and identify brain region-specific proteomic differences within both cell types, some of which might potentially underlie the selective vulnerability to neurological diseases. Leveraging the cellular specificity of proteomic labeling, we apply an antibody-based approach to uncover differences in neuron and astrocyte-derived signaling phospho-proteins and cytokines. This approach will facilitate the characterization of cell-type specific proteomes in a diverse number of tissues under both physiological and pathological states. Current isolation-based approaches for cell type-specific proteomics pose several challenges. Here, the authors present an approach for in vivo cell type-specific protein labeling to characterize proteomic differences between neurons and astrocytes in their native state in adult mouse brain.

The world is awash with claims about the effects of health interventions. Many of these claims are untrustworthy because the bases are unreliable. Acting on unreliable claims can lead to waste of resources and poor health outcomes. Yet, most people lack the necessary skills to appraise the reliability of health claims. The Informed Health Choices (IHC) project aims to equip young people in Ugandan lower secondary schools with skills to think critically about health claims and to make good health choices by developing and evaluating digital learning resources. To ensure that we create resources that are suitable for use in Uganda's secondary schools and can be scaled up if found effective, we conducted a context analysis. We aimed to better understand opportunities and barriers related to demand for the resources, how the learning content overlaps with existing curriculum and conditions in secondary schools for accessing and using digital resources, in order to inform resource development. We used a mixed methods approach and collected both qualitative and quantitative data. We conducted document analyses, key informant interviews, focus group discussions, school visits, and a telephone survey regarding information communication and technology (ICT). We used a nominal group technique to obtain consensus on the appropriate number and length of IHC lessons that should be planned in a school term. We developed and used a framework from the objectives to code the transcripts and generated summaries of query reports in Atlas.ti version 7. Critical thinking is a key competency in the lower secondary school curriculum. However, the curriculum does not explicitly make provision to teach critical thinking about health, despite a need acknowledged by curriculum developers, teachers and students. Exam oriented teaching and a lack of learning resources are additional important barriers to teaching critical thinking about health. School closures and the subsequent introduction of online learning during the COVID-19 pandemic has accelerated teachers' use of digital equipment and learning resources for teaching. Although the government is committed to improving access to ICT in schools and teachers are open to using ICT, access to digital equipment, unreliable power and internet connections remain important hinderances to use of digital learning resources. There is a recognized need for learning resources to teach critical thinking about health in Ugandan lower secondary schools. Digital learning resources should be designed to be usable even in schools with limited access and equipment. Teacher training on use of ICT for teaching is needed.

Claims about what improves or harms our health are ubiquitous. People need to be able to assess the reliability of these claims. We aimed to evaluate an intervention designed to teach primary school children to assess claims about the effects of treatments (ie, any action intended to maintain or improve health). In this cluster-randomised controlled trial, we included primary schools in the central region of Uganda that taught year-5 children (aged 10–12 years). We excluded international schools, special needs schools for children with auditory and visual impairments, schools that had participated in user-testing and piloting of the resources, infant and nursery schools, adult education schools, and schools that were difficult for us to access in terms of travel time. We randomly allocated a representative sample of eligible schools to either an intervention or control group. Intervention schools received the Informed Health Choices primary school resources (textbooks, exercise books, and a teachers' guide). Teachers attended a 2 day introductory workshop and gave nine 80 min lessons during one school term. The lessons addressed 12 concepts essential to assessing claims about treatment effects and making informed health choices. We did not intervene in the control schools. The primary outcome, measured at the end of the school term, was the mean score on a test with two multiple-choice questions for each of the 12 concepts and the proportion of children with passing scores on the same test. This trial is registered with the Pan African Clinical Trial Registry, number PACTR201606001679337. Between April 11, 2016, and June 8, 2016, 2960 schools were assessed for eligibility; 2029 were eligible, and a random sample of 170 were invited to recruitment meetings. After recruitment meetings, 120 eligible schools consented and were randomly assigned to either the intervention group (n=60, 76 teachers and 6383 children) or control group (n=60, 67 teachers and 4430 children). The mean score in the multiple-choice test for the intervention schools was 62·4% (SD 18·8) compared with 43·1% (15·2) for the control schools (adjusted mean difference 20·0%, 95% CI 17·3–22·7; p<0·00001). In the intervention schools, 3967 (69%) of 5753 children achieved a predetermined passing score (≥13 of 24 correct answers) compared with 1186 (27%) of 4430 children in the control schools (adjusted difference 50%, 95% CI 44–55). The intervention was effective for children with different levels of reading skills, but was more effective for children with better reading skills. The use of the Informed Health Choices primary school learning resources, after an introductory workshop for the teachers, led to a large improvement in the ability of children to assess claims about the effects of treatments. The results show that it is possible to teach primary school children to think critically in schools with large student to teacher ratios and few resources. Future studies should address how to scale up use of the resources, long-term effects, including effects on actual health choices, transferability to other countries, and how to build on this programme with additional primary and secondary school learning resources. Research Council of Norway.