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Abstract Objective We describe awareness about the modified “public charge” rule among Oregon’s Mexican-origin Latino/a population and whether concerns about the rule influenced disenrollment from state-funded programs, which do not fall under the public charge. Methods We conducted a cross-sectional survey of adults (ages 18–59) recruited at the Mexican consulate and living in the state of Oregon. Our outcomes were awareness (of the public charge, source of knowledge, and confidence in knowledge of the public charge) and disenrolling self or family members from state-funded public healthcare programs due to concerns about the rule. We described outcomes and used logistic regression and calculated adjusted probabilities to identify factors associated with awareness of the public charge. Results Of 498 Latino/a respondents, 48% reported awareness of the public charge. Among those who knew about the public charge, 14.6% had disenrolled themselves or family members from public healthcare programs and 12.1% were hesitant to seek care due to concerns about the public charge. Younger respondents had a lower adjusted probability of awareness of the public charge (18–24 years: 15.6% (95% CI 3.1–28.2); 30–39 years 54.9% (95% CI 47.7–62.0). Higher education was associated with a higher adjusted probability of awareness of the public charge; ability to speak English was not associated with awareness of the public charge. Conclusion Our study reveals limited awareness about the public charge among Mexican-origin Oregon Latino/as. Outreach and advocacy are essential to ensure Latino/as know their rights to access available state-funded healthcare programs.

ABSTRACT Tetracyclines serve as broad-spectrum antibiotics to treat bacterial infections. The discovery of new tetracycline resistance genes has led to new questions about the underlying mechanisms of resistance, gene transfer, and their relevance to human health. We tracked changes in the abundance of a 55-kbp conjugative transposon (CTn214) carrying tetQ, a tetracycline resistance gene, within a Bacteroides fragilis metagenome-assembled genome derived from shotgun sequencing of microbial DNA extracted from the ileal pouch of a patient with ulcerative colitis. The mapping of metagenomic reads to CTn214 revealed the multi-copy nature of a 17,044-nt region containing tetQ in samples collected during inflammation and uninflamed visits. B. fragilis cultivars isolated from the same patient during periods of inflammation harbored CTn214 integrated into the chromosome or both a circular, multi-copy, extrachromosomal region of the CTn214 containing tetQ and the corresponding integrated form. The tetracycline-dependent mechanism for the transmission of CTn214 is nearly identical to a common conjugative transposon found in the genome of B. fragilis (CTnDOT), but the autonomously amplified nature of a circular 17,044-nt region of CTn214 that codes for tetQ and the integration of the same sequence in the linear chromosome within the same cell is a novel observation. Genome and transcriptome sequencing of B. fragilis cultivars grown under different concentrations of tetracycline and ciprofloxacin indicates that tetQ in strains containing the circular form remains actively expressed regardless of treatment, while the expression of tetQ in strains containing the linear form increases only in the presence of tetracycline.IMPORTANCEThe exchange of antibiotic production and resistance genes between microorganisms can lead to the emergence of new pathogens. In this study, short-read mapping of metagenomic samples taken over time from the illeal pouch of a patient with ulcerative colitis to a Bacteroides fragilis metagenome-assembled genome revealed two distinct genomic arrangements of a novel conjugative transposon, CTn214, that encodes tetracycline resistance. The autonomous amplification of a plasmid-like circular form from CTn214 that includes tetQ potentially provides consistent ribosome protection against tetracycline. This mode of antibiotic resistance offers a novel mechanism for understanding the emergence of pathobionts like B. fragilis and their persistence for extended periods of time in patients with inflammatory bowel disease.

Changes in the sequence of an organism's genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.

BackgroundCyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes.ResultsMembers of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria.ConclusionWe find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.

Evidence from high-income countries suggests that group antenatal care, an alternative service delivery model, may be an effective strategy for improving both the provision and experience of care. Until recently, published research about group antenatal care did not represent findings from low- and middle-income countries, which have health priorities, system challenges, and opportunities that are different than those in high-income countries. Because high-quality evidence is limited, the World Health Organization recommends group antenatal care be implemented only in the context of rigorous research. In 2016 the Global Group Antenatal Care Collaborative was formed as a platform for group antenatal care researchers working in low- and middle-income countries to share experiences and shape future research to accelerate development of a robust global evidence base reflecting implementation and outcomes specific to low- and middle-income countries. This article presents a brief history of the Collaborative's work to date, proposes a common definition and key principles for group antenatal care, and recommends an evaluation and reporting framework for group antenatal care research.

The candidate phyla radiation (CPR) comprises a large monophyletic group of bacterial lineages known almost exclusively based on genomes obtained using cultivation-independent methods. Within the CPR, Gracilibacteria (BD1-5) are particularly poorly understood due to undersampling and the inherent fragmented nature of available genomes. Here, we report the first closed, curated genome of a gracilibacterium from an enrichment experiment inoculated from the Gulf of Mexico and designed to investigate hydrocarbon degradation. The gracilibacterium rose in abundance after the community switched to dominance by Colwellia Notably, we predict that this gracilibacterium completely lacks glycolysis, the pentose phosphate and Entner-Doudoroff pathways. It appears to acquire pyruvate, acetyl coenzyme A (acetyl-CoA), and oxaloacetate via degradation of externally derived citrate, malate, and amino acids and may use compound interconversion and oxidoreductases to generate and recycle reductive power. The initial genome assembly was fragmented in an unusual gene that is hypervariable within a repeat region. Such extreme local variation is rare but characteristic of genes that confer traits under pressure to diversify within a population. Notably, the four major repeated 9-mer nucleotide sequences all generate a proline-threonine-aspartic acid (PTD) repeat. The genome of an abundant Colwellia psychrerythraea population has a large extracellular protein that also contains the repeated PTD motif. Although we do not know the host for the BD1-5 cell, the high relative abundance of the C. psychrerythraea population and the shared surface protein repeat may indicate an association between these bacteria.IMPORTANCE CPR bacteria are generally predicted to be symbionts due to their extensive biosynthetic deficits. Although monophyletic, they are not monolithic in terms of their lifestyles. The organism described here appears to have evolved an unusual metabolic platform not reliant on glucose or pentose sugars. Its biology appears to be centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis. We resolved an unusual repeat region that would be invisible without genome curation. The nucleotide sequence is apparently under strong diversifying selection, but the amino acid sequence is under stabilizing selection. The amino acid repeat also occurs in a surface protein of a coexisting bacterium, suggesting colocation and possibly interdependence.

Background: Lack of racial and ethnic diversity in health research negatively impacts generalizability. We describe Mexican and Mexican American women's willingness to participate in health research in Oregon. Methods: We conducted a survey with Mexican-origin Latinas aged 18?49 years. Our primary outcome was willingness to participate in health research; we also asked sociodemographics and barriers and facilitators to participation. We used logistic regression to identify factors associated with willingness to participate. Results: Of 500 participants, 41% said that they would be willing to participate in health research, 14% said no, and 45% were unsure. In multivariable analyses, past participation in research and speaking English well were independently associated with willingness to participate. Barriers to participation included language, accessibility, and fear of medical procedures. Facilitators included improving future health care, language, and free medical care. Conclusions: Mexican-origin Latinas in Oregon are willing to participate in health research, but many are unsure. Providing study materials in Spanish is a concrete first step to improve recruitment and promote equity and inclusion.

Abstract Since the first discovery of reverse transcriptase in bacteria, and later in archaea, bacterial and archaeal retroelements have been defined by their common enzyme that coordinates diverse functions. Yet, evolutionary refinement has produced distinct retroelements across the tree of microbial life that are perhaps best described in terms of their programmed RNA—a compact sequence that preserves core information for a sophisticated mechanism. From this perspective, reverse transcriptase has been selected as the modular tool for carrying out nature’s instructions in various RNA templates. Beneficial retroelements—those that can provide a fitness advantage to their host—evolved to their extant forms in a wide array of microorganisms and their viruses, spanning nearly all habitats. Within each specialized retroelement class, several universal features seem to be shared across diverse taxa, while specific functional and mechanistic insights are based on only a few model retroelement systems from clinical isolates. Currently, little is known about the diversity of cellular functions and ecological significance of retroelements across different biomes. With increasing availability of isolate, metagenome-assembled, and single-amplified genomes, the taxonomic and functional breadth of prokaryotic retroelements is coming into clearer view. This review explores the recently characterized classes of beneficial, yet accessory retroelements of bacteria and archaea. We describe how these specialized mechanisms exploit a form of fixed mobility, whereby the retroelements do not appear to proliferate selfishly throughout the genome. Moreover, we discuss computational approaches for systematic identification of retroelements from vast sequence repositories and highlight recent discoveries in terms of their apparent distribution and ecological significance in nature. Lastly, we present a new perspective on the eco-evolutionary significance of these genetic elements in marine bacteria and demonstrate approaches that enable the characterization of their environmental diversity through metagenomics.

Objectives To identify whether covid-19 vaccines are associated with menstrual changes in order to address concerns about menstrual cycle disruptions after covid-19 vaccination.Design Global, retrospective cohort study of prospectively collected data.Setting International users of the menstrual cycle tracking application, Natural Cycles.Participants 19 622 individuals aged 18-45 years with cycle lengths of 24-38 days and consecutive data for at least three cycles before and one cycle after covid (vaccinated group; n=14 936), and those with at least four consecutive cycles over a similar time period (unvaccinated group; n=4686).Main outcome measures The mean change within individuals was assessed by vaccination group for cycle and menses length (mean of three cycles before vaccination to the cycles after first and second dose of vaccine and the subsequent cycle). Mixed effects models were used to estimate the adjusted difference in change in cycle and menses length between the vaccinated and unvaccinated.Results Most people (n=15 713; 80.08%) were younger than 35 years, from the UK (n=6222; 31.71%), US and Canada (28.59%), or Europe (33.55%). Two thirds (9929 (66.48%) of 14 936) of the vaccinated cohort received the Pfizer-BioNTech (BNT162b2) covid-19 vaccine, 17.46% (n=2608) received Moderna (mRNA-1273), 9.06% (n=1353) received Oxford-AstraZeneca (ChAdOx1 nCoV-19), and 1.89% (n=283) received Johnson & Johnson (Ad26.COV2.S). Individuals who were vaccinated had a less than one day adjusted increase in the length of their first and second vaccine cycles, compared with individuals who were not vaccinated (0.71 day increase (99.3% confidence interval 0.47 to 0.96) for first dose; 0.56 day increase (0.28 to 0.84) for second dose). The adjusted difference was larger in people who received two doses in a cycle (3.70 days increase (2.98 to 4.42)). One cycle after vaccination, cycle length was similar to before the vaccine in individuals who received one dose per cycle (0.02 day change (99.3% confidence interval −0.10 to 0.14), but not yet for individuals who received two doses per cycle (0.85 day change (99.3% confidence interval 0.24 to 1.46)) compared with unvaccinated individuals. Changes in cycle length did not differ by the vaccine’s mechanism of action (mRNA, adenovirus vector, or inactivated virus). Menses length was unaffected by vaccination.Conclusions Covid-19 vaccination is associated with a small and likely to be temporary change in menstrual cycle length but no change in menses length.

Early pregnancy loss (EPL), or miscarriage, is the most common complication of early pregnancy, and pregnant people experiencing EPL most often seek care from their primary obstetric provider or from an emergency department (ED). However, it is uncommon for providers outside obstetrician-gynecologists to be trained in EPL management, and nursing and support staff are also not often included. This study assessed change in practice following an interprofessional training intervention of self-reported use of manual uterine aspiration for management of EPL in the ED. We conducted a single arm pre-test/post-test interventional study design with a matched sample of pre- and post-test data from participants at 8 academic medical center sites that received a training intervention from the Training, Education & Advocacy in Miscarriage Management project between March 2016 and May 2017. We assessed the provision of EPL services in the ED and provider attitudes about these services. Our sample included 80 faculty physicians, resident physicians, and advanced practice clinicians from 8 academic medical center sites. Our findings demonstrate a positive association between participation in the training intervention and self-reported use of manual uterine aspirator in the ED for management of EPL, as well as increased belief that coordination between departments within the institution was smooth post-training. Our findings suggest that the training intervention was successful in influencing the practice of management of EPL using manual uterine aspiration in the ED, highlighting the importance of engaging EDs in training efforts.

Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life1-5. The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability6-8, are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have defined monophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence.

The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane and CO2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO2. The mats' autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems.

BackgroundDiversity-generating retroelements (DGRs) provide organisms with a unique means for adaptation to a dynamic environment through massive protein sequence variation. The potential scope of this variation exceeds that of the vertebrate adaptive immune system. DGRs were known to exist only in viruses and bacteria until their recent discovery in archaea belonging to the 'microbial dark matter', specifically in organisms closely related to Nanoarchaeota. However, Nanoarchaeota DGR variable proteins were unassignable to known protein folds and apparently unrelated to characterized DGR variable proteins.ResultsTo address the issue of how Nanoarchaeota DGR variable proteins accommodate massive sequence variation, we determined the 2.52 Å resolution limit crystal structure of one such protein, AvpA, which revealed a C-type lectin (CLec)-fold that organizes a putative ligand-binding site that is capable of accommodating 10(13) sequences. This fold is surprisingly reminiscent of the CLec-folds of viral and bacterial DGR variable protein, but differs sufficiently to define a new CLec-fold subclass, which is consistent with early divergence between bacterial and archaeal DGRs. The structure also enabled identification of a group of AvpA-like proteins in multiple putative DGRs from uncultivated archaea. These variable proteins may aid Nanoarchaeota and these uncultivated archaea in symbiotic relationships.ConclusionsOur results have uncovered the widespread conservation of the CLec-fold in viruses, bacteria, and archaea for accommodating massive sequence variation. In addition, to our knowledge, this is the first report of an archaeal CLec-fold protein.

Here, the authors report a large-scale comparative analysis of

El objetivo de esta investigación fue la identificación de las barreras más recurrentes de acceso a abortos en contextos clínicos (clandestinos o legales), desde la perspectiva de acompañantes, activistas feministas que acompañan a mujeres que optaron por abortos autogestionados con medicamentos. Realizamos 14 entrevistas semiestructuradas con acompañantes en tres regiones mexicanas: Baja California y Chiapas, ambos contextos restrictivos, y la Ciudad de México, donde el aborto por voluntad es legal hasta las 12 semanas. Identificamos cuatro categorías en las cuales se entretejen las vulnerabilidades sociales de las mujeres que deciden abortar, la falta de información, persistencia de estigma, y la influencia del marco legal, los fallos en la atención del aborto, incluso en las clínicas de interrupción legal de embarazo (en la Ciudad de México), y mala calidad de los servicios prestados -maltrato, objeción de conciencia y denuncia de los proveedores de salud-, y, por último, los grupos anti-derechos y sus estrategias. En las tres regiones, el acceso a abortos clínicos sigue siendo un privilegio reservado para las mujeres que cuentan con los recursos económicos, logísticos y sociales indispensables para realizarlo en esos espacios. La existencia de un programa Interrupción Legal de Embarazo en solamente una entidad denota la existencia de una desigualdad jurídica y sanitaria. Los hallazgos de este estudio sobre mujeres acompañantes de abortos aportan elementos para que el Estado mexicano mejore el acceso a abortos seguros para todas las mujeres, sobre todo ahora que la Suprema Corte de la Justicia de la Nación decretó la despenalización, y la legalización inminente en todo el país.

Objetivo. Analizar la anticoncepción posparto (APP) y tipo de método anticonceptivo recibido según características sociodemográficas y de atención del parto de las mujeres. Material y métodos. Se analizaron datos de la Encuesta Nacional de Salud y Nutrición (Ensanut) 2018-19 en 4 548 mujeres de 12-49 años que tuvieron un parto. Se ajustaron modelos de regresión logística (n=4 544) y multinomial (n=2 903) con variables dependientes APP y tipo de anticonceptivo recibido. Resultados. Se encontró que 65% de las mujeres recibieron APP, y 56.8% de las adolescentes un método reversible de larga duración (43.7% DIU y 13.1% implantes). Ser indígena, tener un hijo, o recibir atención en los servicios estatales de salud/IMSS-Prospera o privadas, se asocia con menores posibilidades de APP. Conclusiones. Se identificaron progresos en la cobertura de APP en las adolescentes. Persisten brechas de acuerdo con el aseguramiento en salud tanto en la recepción de APP como en el tipo de método recibido.

Abstract Background Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes. Results Members of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria. Conclusion We find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.

Abstract Background CenteringPregnancy (CP) is a group antenatal care (G-ANC) model that has proven beneficial for mothers and their newborns. We conducted a feasibility study beginning in 2016 as part of the Mexican effort to implement G-ANC locally. This study reports on fidelity to the essential elements of CP during its implementation in Mexico. Methods We collected prospective data using a standardized checklist at four primary-care centers that implemented our adapted G-ANC model. We performed a descriptive analysis of fidelity to 28 processes per G-ANC session (71 sessions made up of 10 groups and 129 women across 4 health centers). We calculated fidelity to each process as a proportion with 95% confidence intervals. We present overall results and stratified by health center and by facilitation team. Results Overall fidelity to the G-ANC intervention was 82%, with variability by health center (78–88%). The elements with the highest fidelity were having space for activities such as checking vital signs, conversation in a circle, and medical check-ups (100% each) and the element with the lowest fidelity was using music to enhance privacy (27.3%). Fidelity was not significantly different by center. Conclusions Our study suggests good model fidelity during the implementation of G-ANC in Mexico. Our findings also contribute useful information about where to focus efforts in the future to maintain and improve G-ANC model fidelity.