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BACKGROUND: Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood. RESULTS: Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to "hijack" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts. CONCLUSIONS: This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.
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Metagenoma , Filogenia , Genoma Bacteriano , Sedimentos Geológicos/microbiologia , Genômica , Água do Mar/microbiologia , Organismos Aquáticos/genética , Metabolismo Secundário , MetagenômicaRESUMO
Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay. Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South San Francisco Bay during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in quantitative polymerase chain reaction (PCR) data, and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Candidatus Nitrosomarinus catalina-like AOA metagenome-assembled genome that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria metagenome-assembled genome from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier metagenome-assembled genomes. This study confirms AOA are not only abundant but also highly active during blooms oxidizing large amounts of ammonia to nitrite-a key intermediate in the microbial nitrogen cycle-and producing reactive compounds that may impact other members of the microbial community.
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Amônia , Archaea , Baías , Nitrificação , Oxirredução , Amônia/metabolismo , São Francisco , Archaea/genética , Archaea/classificação , Archaea/metabolismo , Archaea/isolamento & purificação , Baías/microbiologia , Metagenoma , Estações do Ano , MetagenômicaRESUMO
Huntington's disease (HD) is an autosomal dominant disease caused by the expansion of cytosine-adenine-guanine (CAG) repeats in one copy of the HTT gene (mutant HTT, mHTT). The unaffected HTT gene encodes wild-type HTT (wtHTT) protein, which supports processes important for the health and function of the central nervous system. Selective lowering of mHTT for the treatment of HD may provide a benefit over nonselective HTT-lowering approaches, as it aims to preserve the beneficial activities of wtHTT. Targeting a heterozygous single-nucleotide polymorphism (SNP) where the targeted variant is on the mHTT gene is one strategy for achieving allele-selective activity. Herein, we investigated whether stereopure phosphorothioate (PS)- and phosphoryl guanidine (PN)-containing oligonucleotides can direct allele-selective mHTT lowering by targeting rs362273 (SNP3). We demonstrate that our SNP3-targeting molecules are potent, durable, and selective for mHTT in vitro and in vivo in mouse models. Through comparisons with a surrogate for the nonselective investigational compound tominersen, we also demonstrate that allele-selective molecules display equivalent potency toward mHTT with improved durability while sparing wtHTT. Our preclinical findings support the advancement of WVE-003, an investigational allele-selective compound currently in clinical testing (NCT05032196) for the treatment of patients with HD.
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We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (n = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (Methanoregulaceae, Methanotrichaceae, and Methanomassiliicoccales), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (Candidatus Methanoperedens) in anoxic depths and uncultured bacteria (Ca. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. Ca. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the Ca. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured Thermoplasmata archaea in the Ca. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the Ca. Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.
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Sedimentos Geológicos , Metagenoma , Metano , Rios , Metano/metabolismo , Sedimentos Geológicos/microbiologia , Rios/microbiologia , Archaea/genética , Archaea/metabolismo , Archaea/classificação , Bactérias/genética , Bactérias/classificação , Bactérias/metabolismo , Bactérias/isolamento & purificação , Filogenia , Genoma Arqueal , Genoma Bacteriano/genéticaRESUMO
Infantile hemangiomas are commonly encountered at all levels of medical practice. Clinicians should be aware of their typical clinical history and findings in order to expedite early diagnosis and management. It is also necessary to be aware of differential diagnoses that may mimic infantile hemangiomas but have a more concerning prognosis. The objective of this report is to describe the clinical case of one such mimic, dermatofibrosarcoma protuberans. This report highlights key clinical findings of infantile hemangiomas, while also identifying "red flags" that necessitate urgent additional investigations and referral to a multidisciplinary team. Additionally, key features in the management of both infantile hemangiomas and extremity masses are discussed.
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Background: One in every three women worldwide experiences postnatal depression after childbirth, with long-term negative consequences on their children. The mainstream mental healthcare provision for British mothers of African/Caribbean origin is mostly unsuccessful due to a lack of culturally appropriate care. Methods: The study adopts a mixed-methods randomised controlled trial (RCT) design. A 12-session (60 minutes each) of online Learning Through Play plus Culturally adapted Cognitive Behaviour Therapy (LTP+CaCBT) intervention was employed for treating postnatal depression in comparison with psychoeducation (PE). Participants aged 19-53 were screened for depression using the Patient Health Questionnaire (PHQ-9). N=130 participants who scored >5 on PHQ-9 were randomised into LTP+CaCBT (n=65) or PE (n=65) groups. N=12 focus groups (LTP+CaCBT, n=6; PE, n=6) and n=15 individual interviews (LTP+CaCBT, n=8; PE, n=7) were conducted, transcribed verbatim and analysed. Results: Satisfaction with intervention (LTP+CaCBT, 72.9%; PE, 65.2%); retention rates (LTP+CaCBT, 91%; PE, 71%); reduction in postnatal depression was higher in LTP+CaCBT on PHQ-9 Md=1.00 with z= -4.046; compared to PE, Md=1.00 with z= -1.504. Both groups showed reduced levels of anxiety on GAD-7 with no significant difference. Emerging themes from the qualitative findings showed increased positive moods, reduced worries about parenting difficulties and the facilitative role of remote intervention. Conclusions: LTP+CaCBT intervention is culturally appropriate and acceptable and reduces postnatal depression in British mothers of African/Caribbean origin. A fully powered RCT is recommended to evaluate the clinical and cost-effectiveness of LTP+CaCBT, including the child's outcomes compared with routine treatment as usual. Clinical trial registration: www.ClinicalTrials.gov, identifier NCT04820920.
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BACKGROUND: Self-harm and suicidal ideation are increasing public health concerns globally and are paramount in Africa. Therefore, a review of suicidal ideation and self-harm interventions would be beneficial in identifying culturally appropriate interventions for the African context. METHOD: The Population, phenomenon of Interest and Context (PICo) model was adopted to formulate the review strategy. Thus, the Population (Africans), phenomenon of Interest (intervention) and Context (self-harm and suicidal ideation). We used this PICo strategy which is a modified version of PICO for qualitative studies. Framework with Boolean operators (AND/OR/NOT) was further used to ensure rigor through search terms such as ("Suicide" OR "suicidal ideation") AND ("Intervention" OR "Treatment" OR "Therapy" OR "Psychological" OR "Psychosocial" OR "Culturally adapted") AND "Africa" OR "African countries." Six databases were searched (Embase, PsycINFO, ProQuest Central, Cochrane Controlled Trials Register, Medline, and Web of Science) for published articles between 2000 and March 2023. N = 12 studies met the inclusion criteria, and the relevant data extracted were synthesized and thematically analyzed. The review protocol was pre-registered on the PROSPERO Registry (no. CRD42021283795). RESULTS: N = 12 studies met the inclusion criteria, and the following themes emerged from the synthesized literature and analyses of current African approaches to curbing self-harm and suicidal ideation: (a) Western medical and compassion-focused intervention (b) the helpful role of traditional healing and healers (c) psychoeducation and self-help techniques (d) use of technology and a nation-wide approach. CONCLUSION: Self-harm and suicidal ideation are global health concerns. To address this health concern in Africa, the authors recommend culturally adapted psychological interventions to be tested via randomized control trials.
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BACKGROUND: Suicide and self-harm are global disease burden that contributes significantly to years of lost life and mortality. Despite the increasing rates of suicide and self-harm in Nigeria, this topic is understudied. METHODS: A mixed-methods design was adopted. Study 1 interviewed n = 18 participants (n = 11 clinicians; n = 5 patients with a history of self-harm and suicide ideation; and n = 2 caregivers). All interviews were audio-recorded, transcribed verbatim, and analyzed using IPA. Study 2 surveyed n = 562 non-clinical sample about their tolerance toward self-harm and the data was analyzed using One-way ANOVA in SPSS. RESULTS: Study 1 qualitative findings showed substance use, perceived rejection and social isolation were considered predisposing factors for suicide and self-harm. Cultural and religious beliefs shaped help-seeking behaviours. Although Study 2 found no significant differences in demographic characteristics concerning public tolerance toward persons with a history of self-harm, 64% believed that individuals who died by suicide would face punishment after death; 51% believed that victims of attempted suicide are a source of shame to their families; and 33.8% agreed that dying by suicide is the correct behaviour. CONCLUSIONS: Patients with a history of self-harm and suicidal ideation consider family members and close friends as valuable sources of support. Due to the potential clinical implication of cultural and religious beliefs, as shown in the present study's findings, the authors recommend a co-development of culturally appropriate psychological intervention for persons with a history of self-harm and suicidal ideation to be tested in randomized control trials.
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San Francisco Bay (SFB) is a large and highly human-impacted estuarine system. We produced 449 metagenome-assembled genomes from SFB waters, collected along the salinity gradient, providing a rich data set to compare the metabolic potential of microorganisms from different salinity zones within SFB and to other estuarine systems.
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The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 460 highly complete publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided detailed IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.
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Alphaproteobacteria , Águas Salinas , Filogenia , Oceanos e Mares , Genômica , Evolução Biológica , Alphaproteobacteria/genética , Água do MarRESUMO
BACKGROUND: Bipolar Disorders (BDs) are chronic mental health disorders that often result in functional impairment and contribute significantly to the disability-adjusted life years (DALY). BDs are historically under-researched compared to other mental health disorders, especially in Sub-Saharan Africa and Nigeria. DESIGN: We adopted a mixed-methods design. Study 1 examined the public knowledge of BDs in relation to sociodemographic outcomes using quantitative data whilst Study 2 qualitatively assessed the lived experiences of patients with BDs, clinicians, and family caregivers. METHODS: In Study 1, a non-clinical sample of n = 575 participants responded to a compact questionnaire that examined their knowledge of BDs and how they relate to certain sociodemographic variables. One-way ANOVA was used to analyse quantitative data. Study 2 interviewed N = 15 participants (n = 5 patients with BDs; n = 7 clinicians; n = 3 family caregivers). These semi-structured interviews were audio-recorded, transcribed, and thematically analysed. RESULTS: In Study 1, findings showed no statistically significant differences, suggesting low awareness of BDs, especially among vulnerable populations such as young people and older adults. However, there was a trajectory in increased knowledge of BDs among participants between the ages of 25-44 years and part-time workers compared to other ages and employment statuses. In Study 2, qualitative findings showed that BDs are perceived to be genetically and psycho-socially induced by specific lived experiences of patients and their family caregivers. Although psychotropic medications and psychotherapy are available treatment options in Nigeria, cultural and religious beliefs were significant barriers to treatment uptake. CONCLUSIONS: This study provides insight into knowledge and beliefs about BDs, including the lived experiences of patients with BDs, their caregivers and clinicians in Nigeria. It highlights the need for further studies assessing Nigeria's feasibility and acceptability of culturally adapted psychosocial interventions for patients with BDs.
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BACKGROUND: Women are likely to suffer from maternal depression due to childbirth difficulties and parenting responsibilities, leading to long-term negative consequences on their children and families. British mothers of African/Caribbean origin uptake of mental healthcare is low due to the lack of access to culturally appropriate care. METHODS: A mixed-methods randomized controlled feasibility trial was adopted to test the appropriateness and acceptability of Learning Through Play plus Culturally adapted Cognitive Behaviour Therapy (LTP+CaCBT) for treating maternal depression compared with Psychoeducation (PE). Mothers (N = 26) aged 20-55 were screened for depression using the Patient Health Questionnaire (PHQ-9). Those who scored >5 on PHQ-9 were further interviewed using the Revised Clinical Interview Schedule to confirm the diagnosis and randomized into LTP+CaCBT (n = 13) or PE (n = 13) groups. Assessments were taken at baseline, end of the intervention at 3- and 6-months post-randomization. N = 2 focus groups (LTP+CaCBT, n = 12; PE, n = 7) and N = 8 individual interviews were conducted (LTP+CaCBT, n = 4; PE, n = 4). RESULTS: The LTP+CaCBT group showed higher acceptability, feasibility and satisfaction levels than the PE group. Participants experienced the intervention as beneficial to their parenting skills with reduced depression and anxiety in the LTP+CaCBT compared to the PE group. CONCLUSIONS: This is the first feasibility trial of an integrated online parenting intervention for British African and Caribbean mothers. The results indicated that culturally adapted LTP+CaCBT is acceptable and feasible. There is a need to study the clinical and cost-effectiveness of LTP+CaCBT in an appropriately powered randomized control trial and include the child's outcomes. TRIAL REGISTRATION: www. CLINICALTRIALS: gov (no. NCT04820920).
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Depressão , Mães , Criança , Humanos , Feminino , Mães/psicologia , Depressão/terapia , Estudos de Viabilidade , Intervenção Psicossocial , Resultado do Tratamento , Região do CaribeRESUMO
The field of gene editing continues to expand significantly and is entering a time of unprecedented utility. Academia and industry look to conquer genetic-based disease with viral and non-viral-delivered CRISPR-Cas9. The most widely used Cas9 protein is derived from Streptococcus pyrogenes (SpCas9), which lends itself to being too large for AAV viral delivery. Cas9 orthologue proteins have diverse size and dependent on bacteria of origin. This diversity has given rise to Cas9 proteins smaller in size while maintaining gene editing abilities. In this article, authors have focused on the use of CjCas9, whose smaller size allows for packaging in AAV and maintains high on-target gene editing. The locus APOC3 was identified for eventual targeting/integration in humans where cardioprotective properties are predicted. To confirm in vivo targeting of this locus, a humanized mouse model was developed due to the absence of the APOC3 locus in mice. These studies looked to answer long-standing questions on integrated gene stability, promoter/low gene integration, and the duration of therapeutic efficacy of the integrated gene.
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The aim of this review was to assess diagnostic and treatment challenges of adolescents with SI joint pain. We diagnosed 13 of the patients who were referred to our chronic pain clinic because of low back pain (30%) with SI joint pain based on provocative tests response. We performed SI joint steroid infiltration. Six patients (46%) felt better immediately after the procedure and 1 (8%) patient had a one-side only pain relief after a bilateral block. Four of these patients (31%) did not experience any further episode of pain during the follow-up and three patients reported recurring pain on average 2 months after the initial procedure. The 2nd procedure was successful in two patients and the third one experienced pain again 12 months later, requiring a third successful infiltration. Six patients (46%) experienced pain again within a few hours or days after the infiltration and their pain score were unchanged compared with what they had reported prior to the procedure. We were unable to place the needle within the joint under fluoroscopy in 1 patient; however, we were successful repeating the procedure under CT guidance. One patient experienced a motor and sensory block in the distribution of the sciatic nerve immediately after the procedure, which resolved within 24 and 48 hours, respectively. SI joint pain is a distinctive pathology that can be present in children and adolescents and is often overlooked by practitioners. Its diagnosis and management are challenging in this population as it is in adults. SI joint steroids injections may play a role in the management of these patients.
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Second messenger signaling is required for cellular processes. We previously reported that extracellular vesicles (EVs) from stimulated cultured endothelial cells contain the biochemical second messenger, cAMP. In the current study, we sought to determine whether cAMP-enriched EVs induce second messenger signaling pathways in naïve recipient cells. Our results indicate that cAMP-enriched EVs increase cAMP content sufficient to stimulate PKA activity. The implications of our work are that EVs represent a novel intercellular mechanism for second messenger, specifically cAMP, signaling.
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AMP Cíclico , Vesículas Extracelulares , Células Cultivadas , AMP Cíclico/metabolismo , Células Endoteliais/metabolismo , Vesículas Extracelulares/metabolismo , Sistemas do Segundo Mensageiro , Transdução de SinaisRESUMO
Purpose In this study, we aimed to compare axial length (AL) measurements of the IOLMaster 500 (Carl Zeiss Meditec AG, Jena, Germany), based on partial coherence interferometry (PCI) versus the Aladdin (Topcon Healthcare, Oakland, NJ), based on optical low-coherence interferometry (OLCI), in a clinical setting. Methods A retrospective analysis of the records of patients presenting for cataract surgery at an ophthalmology practice between October 2019 and March 2020 was performed. All patients had biometry measurements on the IOLMaster 500 and the Aladdin. Data collected included patient demographics, cataract morphology and type, and AL measurements. The IOLMaster 500 and Aladdin measurements were compared using the unpaired t-test and Chi-squared test. Results In total, 393 eyes (197 patients) were included (91 males, 107 females) in the study. The IOLMaster 500 was unable to successfully obtain AL measurements in seven eyes (1.8%) and the Aladdin in 26 eyes (6.6%). The difference was statistically significant (p=0.0007). Advanced and central posterior subcapsular cataracts were common in eyes that had unsuccessful measurements. In the eyes successfully measured, the mean AL for the IOLMaster was 24.04 ±1.32 mm, while it was 24.04 ±1.34 mm for the Aladdin. However, this difference was not statistically significant (p=0.9165). Conclusion The IOLMaster 500 performed better in terms of the number of eyes for which AL measurements were successfully obtained compared to the Aladdin. This may be partly related to high volumes of advanced cataracts treated at our practice. However, this being a retrospective study, a cause-and-effect relationship could not be established.
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Alternative splicing is frequently involved in the diversification of protein function and can also be modulated for therapeutic purposes. Here we develop a predictive model, called Exon ByPASS (predicting Exon skipping Based on Protein amino acid SequenceS), to assess the criticality of exon inclusion based solely on information contained in the amino acid sequence upstream and downstream of the exon junctions. By focusing on protein sequence, Exon ByPASS predicts exon skipping independent of tissue and species in the absence of any intronic information. We validate model predictions using transcriptomic and proteomic data and show that the model can capture exon skipping in different tissues and species. Additionally, we reveal potential therapeutic opportunities by predicting synthetically skippable exons and neo-junctions arising in cancer cells.
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Processamento Alternativo , Proteômica , Sequência de Aminoácidos , Éxons/genética , ÍntronsRESUMO
Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of "Candidatus Nitrosomarinus catalina" SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 µM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB. IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)-the largest estuary on the west coast of North America-and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.
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Amônia , Archaea , Metagenômica , Baías , Metagenoma , São Francisco , RNA Ribossômico 16S , Estações do Ano , Nitritos , Urease/genética , Oxirredução , Sedimentos Geológicos/microbiologia , Água , NitrogênioRESUMO
The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.
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Archaea , Metagenômica , Amônia/metabolismo , Archaea/metabolismo , Sedimentos Geológicos , Oxirredução , Filogenia , SoloRESUMO
The goal of this study was to evaluate hepatocyte-specific gene editing, via systemic administration of hyaluronic acid (HA)-based nanoparticles in naïve CD-1 mice. Using HA-poly(ethylene imine) (HA-PEI) and HA-PEI-mannose nanoparticles with differential mannose density (1X and 2X), we have evaluated systemic biodistribution and hepatocyte-specific delivery using IVIS imaging and flow cytometry. Additionally, we have investigated hepatocyte-specific delivery and transfection of CRISPR/Cas9 gene editing plasmid and eGFP gene payload to integrate at the Rosa26 locus. IVIS imaging showed uptake of HA-PEI nanoparticles primarily by the liver, and with addition of mannose at different concentrations, the nanoparticles showed increased uptake in both the liver and spleen. HA-PEI-mannose nanoparticles showed 55-65% uptake by hepatocytes, along with uptake by resident macrophage regardless of the mannose concentration. One of two gRNA targets showed 15% genome editing and obtained similar results for all three nanoparticle formulations. Cells positive for our gene payload were greatest with HA-PEI-mannose-1X nanoparticles where 16.2% of cells were GFP positive. The results were encouraging as proof of concept for the development of a non-viral biodegradable and biocompatible polymeric delivery system for gene editing specifically targeting hepatocytes upon systemic administration.