Summary
The widespread unicellular cyanobacteria Synechococcus are major contributors to global marine primary production. Here, we report their abundance, phylogenetic diversity (as assessed using ...the RNA polymerase gamma subunit gene rpoC1) and pigment diversity (as indirectly assessed using the laterally transferred cpeBA genes, encoding phycoerythrin‐I) in surface waters of the northwestern Pacific Ocean, sampled over nine distinct cruises (2008–2015). Abundance of Synechococcus was low in the subarctic ocean and South China Sea, intermediate in the western subtropical Pacific Ocean, and the highest in the Japan and East China seas. Clades I and II were by far the most abundant Synechococcus lineages, the former dominating in temperate cold waters and the latter in (sub)tropical waters. Clades III and VI were also fairly abundant in warm waters, but with a narrower distribution than clade II. One type of chromatic acclimater (3dA) largely dominated the Synechococcus communities in the subarctic ocean, while another (3dB) and/or cells with a fixed high phycourobilin to phycoerythrobilin ratio (pigment type 3c) predominated at mid and low latitudes. Altogether, our results suggest that the variety of pigment content found in most Synechococcus clades considerably extends the niches that they can colonize and therefore the whole genus habitat.
Viruses and dissolved organic matter (DOM) are major top–down and bottom–up factors, respectively, which control the abundance and diversity of bacterial communities. However, the relative strength ...and interaction between these two regulators in different marine ecosystems are not fully understood. We applied viral reduction and cross-transplantation of eutrophic estuarine and pristine coastal waters to examine the separate and combined effects of viruses and DOM on the bacterial community composition. We showed that bacteria were more abundant in the virus-depleted groups, particularly in those from the eutrophic estuarine water (i.e.,> 7 times higher, when compared with the virus-rich groups). Cluster analyses showed that the bacterial communities in the virus-rich groups were most similar to the in situ populations. Bacterial community richness, evenness and diversity were reduced at high DOM concentrations but were sustained by viruses. This allowed bacteria that were less vulnerable to viral infection to thrive (such as those in the families Alteromonadaceae, Rhodobacteraceae, Flavobacteriaceae, and SAR11), while suppressing those capable of fast growth at elevated DOM concentrations but which were more vulnerable to viral attack (such as those from the family Vibrionaceae). Our results showed that viral regulation occurring at the strain level can affect the bacterial community structure at higher phylogenetic levels. In addition, some less abundant groups, such as Vibrio and Alteromonas, might actually win the competition for resources, providing viral control is removed. Our results also showed that the population dynamics of certain bacterial groups was controlled by viruses, and the strength of such control was modulated by the concentration of DOM. We suggest that the composition of the bacterial community in aquatic environments results from the interactive regulation by DOM and viruses among other regulators.
Single-cell RNA sequencing (scRNA-seq) is an important tool for understanding disease pathophysiology, including airway diseases. Currently, the majority of scRNA-seq studies in airway diseases have ...used invasive methods (airway biopsy, surgical resection), which carry inherent risks and thus present a major limitation to scRNA-seq investigation of airway pathobiology. Bronchial brushing, where the airway mucosa is sampled using a cytological brush, is a viable, less invasive method of obtaining airway cells for scRNA-seq. Here we describe the development of a rapid and minimal handling protocol for preparing single-cell suspensions from bronchial brush specimens for scRNA-seq. Our optimized protocol maximizes cell recovery and cell quality and facilitates large-scale profiling of the airway transcriptome at single-cell resolution.
We present a protocol for preparing single-cell suspensions from bronchial brushes for single-cell RNA sequencing that is fast, involves minimal handling, produces high cell yield/quality and is easily scalable due to efficiency and simplicity.
The classical M1/M2 polarity of macrophages may not be applicable to inflammatory lung diseases including chronic obstructive pulmonary disease (COPD) due to the complex microenvironment in lungs and ...the plasticity of macrophages. We examined macrophage sub-phenotypes in bronchoalveolar lavage (BAL) fluid in 25 participants with CD40 (a M1 marker) and CD163 (a M2 marker). Of these, we performed RNA-sequencing on each subtype in 10 patients using the Illumina NextSeq 500. Approximately 25% of the macrophages did not harbor classical M1 or M2 surface markers (double negative, DN), and these cells were significantly enriched in COPD patients compared with non-COPD patients (46.7% vs. 14.5%, p < 0.001). 1886 genes were differentially expressed in the DN subtype compared with all other subtypes at a 10% false discovery rate. The 602 up-regulated genes included 15 mitochondrial genes and were enriched in 86 gene ontology (GO) biological processes including inflammatory responses. Modules associated with cellular functions including oxidative phosphorylation were significantly down-regulated in the DN subtype. Macrophages in the human BAL fluid, which were negative for both M1/M2 surface markers, harbored a gene signature that was pro-inflammatory and suggested dysfunction in cellular homeostasis. These macrophages may contribute to the pathogenesis and manifestations of inflammatory lung diseases such as COPD.
•What is currently known about this topic?Although a well-established concept in adult surgery, the effects of ERAS on the short- and long-term perioperative outcomes in paediatric gastrointestinal ...surgery are rapidly evolving.•What new information is contained in this article?Our review summarises the newest evidence on this topic, suggesting the role of ERAS in improving perioperative outcomes such as length of stay and postoperative gastrointestinal functions. Potential topics for future studies are also outlined.
Implementing Enhanced Recovery After Surgery (ERAS) protocols has been shown to improve perioperative outcomes in adults undergoing gastrointestinal surgeries. Herewith, we performed a scoping review to evaluate the practice of ERAS protocol in paediatric patients undergoing gastrointestinal surgeries.
PubMed, Medline (Ovid), Scopus, and Cochrane Library were searched. Studies investigating the effect of adopting an ERAS protocol on children undergoing gastrointestinal surgeries are included. Data on the study design, operative procedures, ERAS element, and surgical outcomes were evaluated. Elements of ERAS were also examined.
among the 15 included papers, patients under an ERAS protocol have shorter length of stay (n = 11); better postoperative gastrointestinal function in terms of time to any (n = 5) or regular amount of diet (n = 5), shorter time to first defaecation (n = 4), and less requirement of parenteral nutrition (n = 2); and less opioid use in the intraoperative (n = 4) and postoperative (n = 5) periods. An average of 9.67 ERAS elements are adopted in the studies with the commonest being providing information and education to the patient and family (n = 12).
ERAS protocols have apparent benefits for children undergoing gastrointestinal surgeries with improved perioperative outcomes. Evidence from higher quality study is warranted to confirm this relationship in detail and to enhance the applicability.
This is a review study, hence not applicable
The associations between airway eosinophilia, measured in sputum or peripheral blood, and acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are inconsistent. We therefore aimed to ...determine the association between eosinophilia in bronchoalveolar lavage (BAL) fluid and AECOPD in a clinical cohort. We analyzed differential cell counts from baseline BAL fluid in participants in the DISARM clinical trial (Clinicaltrials.gov #NCT02833480) and classified participants by the presence or absence of BAL eosinophilia (>1% of total leukocytes). We determined the association between BAL eosinophilia and AECOPD over 1 year of follow-up using negative binomial regression and Cox proportional hazards test. N = 63 participants were randomized, and N = 57 had BAL differential cell counts available. Participants with BAL eosinophilia (N = 21) had a significantly increased rate of acute exacerbations (unadjusted incidence rate ratio (IRR) 2.0, p = 0.048; adjusted IRR 2.24, p = 0.04) and a trend toward greater probability of acute exacerbation (unadjusted hazard ratio (HR) 1.74, p = 0.13; adjusted HR 2.3, p = 0.1) in the year of follow-up compared to participants without BAL eosinophilia (N = 36). These associations were not observed for BAL neutrophilia (N = 41 participants), BAL lymphocytosis (N = 27 participants) or peripheral blood eosinophilia at various threshold definitions (2%, N = 37; 3%, N = 27; 4%, N = 16). BAL may therefore be a sensitive marker of eosinophilic inflammation in the distal lung and may be of benefit for risk stratification or biomarker-guided therapy in COPD.
Ecosystem models need to capture biodiversity, because it is a fundamental determinant of food web dynamics and consequently of the cycling of energy and matter in ecosystems. In oceanic food webs, ...the plankton compartment encompasses by far most of the biomass and diversity. Therefore, capturing plankton diversity is paramount for marine ecosystem modelling. In recent years, many models have been developed, each representing different aspects of plankton diversity, but a systematic comparison remains lacking. Here we present established modelling approaches to study plankton ecology and diversity, discussing the limitations and strengths of each approach. We emphasize their different spatial and temporal resolutions and consider the potential of these approaches as tools to address societal challenges. Finally, we make suggestions as to how better integration of field and experimental data with modelling could advance understanding of both plankton biodiversity specifically and more broadly the response of marine ecosystems to environmental change, including climate change.
Background
With increasing number of clinical trials relating to fecal microbiota transplantation (FMT), it is crucial to identify and recruit long‐term, healthy, and regular fecal donors.
Objective
...We aimed to report the outcomes of screening and recruitment of fecal donors for FMT.
Methods
Potential donors were recruited via advertisement through internal mass emails at a university. They were required to undergo a pre‐screening telephone interview, a detailed questionnaire, followed by blood and stool investigations.
Results
From January 2017 to December 2020, 119 potential donors were assessed with 75 failed pre‐screening. Reasons for failure included: inability to come back for regular and long‐term donation (n = 19), high body mass index (n = 17), underlying chronic illness or on long‐term medications (n = 11), being healthcare professionals (n = 10), use of antibiotics within 3 months (n = 5) and others (n = 13). Forty‐four donors completed questionnaires and 11 did not fulfill the clinical criteria. Of the remaining 33 potential donors who had stool and blood tests, 21 failed stool investigations (19 extended‐spectrum beta‐lactamase ESBL organisms, one Clostridioides difficile, one C. difficile plus Methicillin Resistant Staphylococcus aureus), one failed blood tests (high serum alkaline phosphatase level), one required long‐term medication and nine withdrew consent and/or lost to follow‐up. In total, only one out of 119 (0.8%) potential donors was successfully recruited as a regular donor.
Conclusion
There was a high failure rate in donor screening for FMT. Main reasons for screening failure included high prevalence of positive ESBL organisms in stool and failed commitment to regular stool donation.
Large amounts of dust and atmospheric aerosols, originating from surrounding desert areas (e.g., Sahara and Middle East) are deposited annually on the surface of the Eastern Mediterranean Sea. These ...depositions can provide high amounts of micro (such as Fe, Zn, Co) and macro nutrients (such as P and N) to supplement nutrient-poor surface waters- that typically limit primary productivity and also dinitrogen (N2) fixation in many marine environments. Here, we studied the impact of the atmospheric deposition of dust and aerosols on N2 fixation in the Cretan Sea (Eastern Mediterranean Sea). Mixed polluted aerosols (hereafter A) and Saharan dust (hereafter SD) were added to nine mesocosms (3-m3 each) containing surface mixed layer seawater (~10 m), and N2 fixation was evaluated for 6 days during May 2012 (springtime). The addition of SD triggered a rapid (30 h) and robust (2-4 fold) increase in N2 fixation rates that remained high for 6 days and contributed 3-8% of the primary productivity. The A addition also resulted in higher N2 fixation rates compared to the unamended control mesocosms, although the responses were less profound (1.5-2 fold) and accounted for only 2-4% of the primary productivity. The microbial community responded differently to the two additions. Heterotrophic bacterial N2 fixers dominated the diazotroph community in A and the control mesocosms, while the non-filamentous cyanobacterial group Trichodesmium prevailed in the SD treatment (68% of all the operational taxonomic units, verified by qPCR analyses). Our results indicate that the aerosol source, its route prior to deposition, and its specific chemical composition, can alter the diazotrophic diversity and activity in the Eastern Mediterranean Sea and may thus impact both the N and C dynamics in this impoverished environment.
In a fair multicast video distribution scheme each receiver should receive a video stream with a quality that is commensurate with its capabilities or the capabilities of the path leading to it, ...regardless of other receivers or network paths. This fairness problem results from the fact that multicast communication trades economy of bandwidth with granularity of control. Distributing video using individual feedback-controlled point-to-point streams results in high bandwidth utilization but the granularity of control is high as communication parameters can be negotiated individually with each receiver. In contrast, using a single multicast stream has good bandwidth economy, but very low granularity of control. In this paper we propose, implement and experiment with a system that spans the spectrum represented by the two extremes above. In the scheme, called destination set grouping (DSG), a source maintains a small number of video streams, carrying the same video but each targeted at receivers with different capabilities. Each stream is feedback-controlled within prescribed limits by its group of receivers. Receivers may move among streams as their capabilities or the capabilities of the network paths leading to them change. The scheme is shown to improve fairness significantly at a small bandwidth cost.
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