2,315 research outputs found

    Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels

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    Background Inflammatory bowel disease (IBD), is a debilitating group of chronic diseases including Crohn’s Disease (CD) and ulcerative colitis (UC), which causes inflammation of the gut and affects millions of people worldwide. At different taxonomic levels, the structure of the gut microbiota is significantly altered in IBD patients compared to that of healthy individuals. However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale. Results In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. A substantial imbalance was observed across four major bacterial phyla including Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria, which together constitute >98% of the gut microbiota. Next, we reconstructed a bacterial family co-abundance network based on the correlation of abundance profiles obtained from the public gut microbiome data of >22000 samples of faecal and gut biopsies taken from both diseased and healthy individuals. The data was compiled using the EBI metagenomics database [1]. By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions. Conclusions IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD

    Design of a Low-Cost Autoclave for Developing World Health Clinics

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    Incidence of surgical site infection is 2–5 times higher in developing nations as compared to developed nations. A low-cost, easy to use autoclave was designed to address the unique technical, behavioral, and market challenges present in rural, health posts of the developing world. A thorough stakeholder analysis was performed very early in the design process to address non-technical needs for sustained user adoption as well as manufacturability and scalability. Twelve partnering clinics in Nepal trialed these autoclaves from July until December 2012. Usage statistics and follow-up observations highlight important factors for successful adoption. These findings were used to improve the autoclave design. The goal of this paper is to detail a case study and methodology to incorporate multiple stakeholder needs into the early design process.MIT IDEAS Global ChallengeMassachusetts Institute of Technology. Priscilla King Gray Public Service CenterMIT International Development Initiativ

    ENERGY REQUIREMENT OF ALTERNATIVE TECHNOLOGIES FOR DESALINATING GROUNDWATER FOR IRRIGATION

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    Increased global water demand coupled with limited water resources has led to acute water shortage in many regions, significantly affecting a griculture, which is the world’s largest consumer of water. Groundwater resources are thus increasingly being used to meet irrigation requirements. However, groundwater resources around the world tend to be saline ( 0.5 ≤ S ≤ 5 g/kg ) rquiring desalination before use. Furthermore, with decreasing water availability, demands for producing permeate from the feed at higher recoveries (>85%) is also increasing. In this work, a thermodynamic least work analysis for desalination and pumping ground water is developed first. Then, the actual energy required by high recovery desalination technologies such as brackish water reverse osmosis (RO), closed circuit reverse osmosis (CCRO) and electrodialysis reversal (EDR) are compared with the thermodynamic least work of desalination from 50-95% recovery. CCRO consumed the least energy until a recovery of 92% after which EDR consumed the least energy. While the energy required for RO and CCRO changed with recovery, EDR energy consumption remained approximately constant at 0.85 kWh/m³. Water table depth was also found to significantly contribute to the total energy consumed, with the power required to pump groundwater being comparable to the desalination power requirements at water table depths greater than 50 m. Thus, the choice of selection of desalination technologies is particularly crucial for water table depths less than 50 m

    Analisis Unit Cost Pelayanan Rawat Inap Postpartum Di Rumah Sakit Umum Dewi Sartika Dengan Menggunakan Metode Activity Based Costing (ABC) System

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    Iklim kompetitif tidak hanya terjadi pada Perusahaan yang berorientasi profit, namun juga berdampak padaperusahaan yang berorientasi nonprofit, salah satunya adalah rumah sakit. Rumah sakit yang berada di SulawesiTenggara pada tahun 2014 berjumlah 36, sedangkan kota Kendari memiliki 13 rumah sakit dan harus melayani347.496 penduduk. Hal ini menjadikan persaingan bisnis rumah sakit baik umum maupun swasta kini semakinketat. Salah satu solusi untuk memenangkan persaingan adalah dengan cara menentukan tarif yang lebih rendahdan kualitas atau jasa yang lebih tinggi dari pada pesaing. Solusi tersebut tentunya menjadikan biaya operasionalrumah sakit akan semakin besar sehingga sistem akuntansi manajemen di rumah sakit harus efektif dan efisiensehingga menghasilkan informasi yang akurat dalam pengambilan keputusan. Rumah sakit cenderung masihmenggunakan system akuntansi tradisional yang memiliki distorsi biaya. Penelitian ini menganalisis perhitungantarif rawat inap pelayanan postpartum di RSU Dewi Sartika menggunakan metode activity based costing system.Penelitian ini menggunakan metode deskriptif komparatif dengan pendekatan kuantitatif, data yang digunakanadalah seluruh data keuangan pada Oktober 2015-September 2016 dan aktivitas yang diobservasi yaitu ruangperawatan kelas VIP, kelas I, kelas II, kelas III dan bangsal. Hasil perhitungan menunjukkan hasil yang berbeda daritarif yang diterapkan. Tarif kelas VIP, kelas I dan kelas III lebih rendah dari tarif rumah sakit sedangkan tarif kelas IIdan bangsal lebih tinggi

    Mining for nonribosomal peptide synthetase and polyketide synthase genes revealed a high level of diversity in the sphagnum bog metagenome

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    Sphagnum bog ecosystems are one of the oldest vegetation forms harbouring a specific microbial community, which is known to produce an exceptionally wide variety of bioactive substances. Although the Sphagnum metagenome indicate a rich secondary metabolism, the genes are not yet explored. To analyse non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) the diversity of NRPS and PKS genes in Sphagnum-associated metagenome was investigated by in silico data mining and sequence-based screening (PCR-amplification of 9500 fosmid clones). The in silico Illumina-based metagenomic approach resulted in the identification of 279 NRPS, 346 PKS, as well as 40 PKS-NRPS hybrid gene sequences. Occurrence of NRPS sequences was strongly dominated by the phyla Protebacteria, especially by the genus Burkholderia, while PKS sequences were mainly affiliated to Actinobacteria. Thirteen novel NRPS-related sequences were identified by PCR-amplification screening, displaying amino acid sequence identities of 48 to 91% to annotated sequences of the phyla Proteobacteria, Actinobacteria and Cyanobacteria. Some of the identified metagenomic clones showed closest similarity to peptide synthases from Burkholderia or Lysobacter, which are emerging bacterial sources of yet undescribed bioactive metabolites. This study highlights the role of the extreme natural ecosystems as a promising source for detection of secondary compounds and enzymes, serving as a source for biotechnological applications

    Trace levels of sewage effluent are sufficient to increase class 1 integron prevalence in freshwater biofilms without changing the core community

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    Most river systems are impacted by sewage effluent. It remains unclear if there is a lower threshold to the concentration of sewage effluent that can significantly change the structure of the microbial community and its mobile genetic elements in a natural river biofilm. We used novel in situ mesocosms to conduct replicated experiments to study how the addition of low-level concentrations of sewage effluent (nominally 2.5 ppm) affects river biofilms in two contrasting Chalk river systems, the Rivers Kennet and Lambourn (high/low sewage impact, respectively). 16S sequencing and qPCR showed that community composition was not significantly changed by the sewage effluent addition, but class 1 integron prevalence (Lambourn control 0.07% (SE ± 0.01), Lambourn sewage effluent 0.11% (SE ± 0.006), Kennet control 0.56% (SE ± 0.01), Kennet sewage effluent 1.28% (SE ± 0.16)) was significantly greater in the communities exposed to sewage effluent than in the control flumes (ANOVA, F = 5.11, p = 0.045) in both rivers. Furthermore, the difference in integron prevalence between the Kennet control (no sewage effluent addition) and Kennet sewage-treated samples was proportionally greater than the difference in prevalence between the Lambourn control and sewage-treated samples (ANOVA (interaction between treatment and river), F = 6.42, p = 0.028). Mechanisms that lead to such differences could include macronutrient/biofilm or phage/bacteria interactions. Our findings highlight the role that low-level exposure to complex polluting mixtures such as sewage effluent can play in the spread of antibiotic resistance genes. The results also highlight that certain conditions, such as macronutrient load, might accelerate spread of antibiotic resistance genes

    Hyper-Methylated Loci Persisting from Sessile Serrated Polyps to Serrated Cancers

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    Although serrated polyps were historically considered to pose little risk, it is now understood that progression down the serrated pathway could account for as many as 15%–35% of colorectal cancers. The sessile serrated adenoma/polyp (SSA/P) is the most prevalent pre-invasive serrated lesion. Our objective was to identify the CpG loci that are persistently hyper-methylated during serrated carcinogenesis, from the early SSA/P lesion through the later cancer phases of neoplasia development. We queried the loci hyper-methylated in serrated cancers within our rightsided SSA/Ps from the New Hampshire Colonoscopy Registry, using the Illumina Infinium Human Methylation 450 k panel to comprehensively assess the DNA methylation status. We identified CpG loci and regions consistently hyper-methylated throughout the serrated carcinogenesis spectrum, in both our SSA/P specimens and in serrated cancers. Hyper-methylated CpG loci included the known the tumor suppressor gene RET (p = 5.72 x 10−10), as well as loci in differentially methylated regions for GSG1L, MIR4493, NTNG1, MCIDAS, ZNF568, and RERG. The hyper-methylated loci that we identified help characterize the biology of SSA/P development, and could be useful as therapeutic targets, or for future identification of patients who may benefit from shorter surveillance intervals

    Expanding the Repertoire of Carbapenem-Hydrolyzing Metallo-ß-Lactamases by Functional Metagenomic Analysis of Soil Microbiota

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    Carbapenemases are bacterial enzymes that hydrolyze carbapenems, a group of last-resort β-lactam antibiotics used for treatment of severe bacterial infections. They belong to three β-lactamase classes based amino acid sequence (A, B, and D). The aim of this study was to elucidate occurrence, diversity and functionality of carbapenemase-encoding genes in soil microbiota by functional metagenomics. Ten plasmid libraries were generated by cloning metagenomic DNA from agricultural (n = 6) and grassland (n = 4) soil into Escherichia coli. The libraries were cultured on amoxicillin-containing agar and up to 100 colonies per library were screened for carbapenemase production by CarbaNP test. Presumptive carbapenemases were characterized with regard to DNA sequence, minimum inhibitory concentration (MIC) of β-lactams, and imipenem hydrolysis. Nine distinct class B carbapenemases, also known as metallo-beta-lactamases (MBLs), were identified in six soil samples, including two subclass B1 (GRD23-1 and SPN79-1) and seven subclass B3 (CRD3-1, PEDO-1, GRD33-1, ESP-2, ALG6-1, ALG11-1, and DHT2-1). Except PEDO-1 and ESP-2, these enzymes were distantly related to any previously described MBLs (33 to 59% identity). RAIphy analysis indicated that six enzymes (CRD3-1, GRD23-1, DHT2-1, SPN79-1, ALG6-1, and ALG11-1) originated from Proteobacteria, two (PEDO-1 and ESP-2) from Bacteroidetes and one (GRD33-1) from Gemmatimonadetes. All MBLs detected in soil microbiota were functional when expressed in E. coli, resulting in detectable imipenem-hydrolyzing activity and significantly increased MICs of clinically relevant β-lactams. Interestingly, the MBLs yielded by functional metagenomics generally differed from those detected in the same soil samples by antibiotic selective culture, showing that the two approaches targeted different subpopulations in soil microbiota. © 2016 Gudeta, Bortolaia, Pollini, Docquier, Rossolini, Amos, Wellington and Guardabassi.Grant HEALTH-F3-2011-282004(EvoTAR
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