Carbohydrate catabolic flexibility in the mammalian intestinal commensal Lactobacillus ruminis revealed by fermentation studies aligned to genome annotations

peer-reviewedBackground: Lactobacillus ruminis is a poorly characterized member of the Lactobacillus salivarius clade that is part of the intestinal microbiota of pigs, humans and other mammals. Its variable abundance in human and animals may be linked to historical changes over time and geographical differences in dietary intake of complex carbohydrates. Results: In this study, we investigated the ability of nine L. ruminis strains of human and bovine origin to utilize fifty carbohydrates including simple sugars, oligosaccharides, and prebiotic polysaccharides. The growth patterns were compared with metabolic pathways predicted by annotation of a high quality draft genome sequence of ATCC 25644 (human isolate) and the complete genome of ATCC 27782 (bovine isolate). All of the strains tested utilized prebiotics including fructooligosaccharides (FOS), soybean-oligosaccharides (SOS) and 1,3:1,4-β-D-gluco-oligosaccharides to varying degrees. Six strains isolated from humans utilized FOS-enriched inulin, as well as FOS. In contrast, three strains isolated from cows grew poorly in FOS-supplemented medium. In general, carbohydrate utilisation patterns were strain-dependent and also varied depending on the degree of polymerisation or complexity of structure. Six putative operons were identified in the genome of the human isolate ATCC 25644 for the transport and utilisation of the prebiotics FOS, galacto-oligosaccharides (GOS), SOS, and 1,3:1,4-β-D-Gluco-oligosaccharides. One of these comprised a novel FOS utilisation operon with predicted capacity to degrade chicory-derived FOS. However, only three of these operons were identified in the ATCC 27782 genome that might account for the utilisation of only SOS and 1,3:1,4-β-D-Gluco-oligosaccharides. Conclusions: This study has provided definitive genome-based evidence to support the fermentation patterns of nine strains of Lactobacillus ruminis, and has linked it to gene distribution patterns in strains from different sources. Furthermore, the study has identified prebiotic carbohydrates with the potential to promote L. ruminis growth in vivo

Control of Water Infiltration into Near Surface LLW Disposal Units. Progress Report on Field Experiments at a Humid Region Site, Beltsville, Maryland: Volume 8

This study`s objective is to assess means for controlling water infiltration through waste disposal unit covers in humid regions. Experimental work is being performed in large-scale lysimeters 21.34 m x 13.72 m x 3.05 m (75 ft x 45 ft x 10 ft) at Beltsville, Maryland. Results of the assessment are applicable to disposal of low-level radioactive waste (LLW), uranium mill tailings, hazardous waste, and sanitary landfills. Three kinds of waste disposal unit covers or barriers to water infiltration are being investigated: (1) resistive layer barrier, (2) conductive layer barrier, and (3) bioengineering management. The resistive layer barrier consists of compacted earthen material (e.g., clay). The conductive layer barrier consists of a conductive layer in conjunction with a capillary break. As long as unsaturated flow conditions are maintained, the conductive layer will wick water around the capillary break. Below-grade layered covers such as (1) and (2) will fail if there is appreciable subsidence of the cover, and remedial action for this kind of failure will be difficult. A surface cover, called bioengineering management, is meant to overcome this problem. The bioengineering management surface barrier is easily repairable if damaged by subsidence; therefore, it could be the system of choice under active subsidence conditions. The bioengineering management procedure also has been shown to be effective in dewatering saturated trenches and could be used for remedial action efforts. After cessation of subsidence, that procedure could be replaced by a resistive layer barrier or, perhaps even better, by a resistive layer barrier/conductive layer barrier system. The latter system would then give long-term effective protection against water entry into waste without institutional care

Influence of the annealing ambient on structural and optical properties of rare earth implanted GaN

GaN films were implanted with Er and Eu ions and rapid thermal annealing was performed at 1000, 1100 and 1200 ⁰C in vacuum, in flowing nitrogen gas or a mixture of NH₃ and N₂. Rutherford backscattering spectrometry in the channeling mode was used to study the evolution of damage introduction and recovery in the Ga sublattice and to monitor the rare earth profiles after annealing. The surface morphology of the samples was analyzed by scanning electron microscopy and the optical properties by room temperature cathodoluminescence (CL). Samples annealed in vacuum and N₂ already show the first signs of surface dissociation at 1000 ⁰C. At higher temperature, Ga droplets form, at the surface. However, samples annealed in NH₃+N₂ exhibit a very good recovery of the lattice along with a smooth surface. These samples also show the strongest CL intensity for the rare earth related emissions in the green (for Er) and red (for Eu). After annealing at 1200 ⁰C in NH₃+N₂ the Eu implanted sample reveals the channeling qualities of an unimplanted sample and a strong increase of CL intensity is observed

Exosomes: From potential culprits to new therapeutic promise in the setting of cardiac fibrosis

Fibrosis is a significant global health problem associated with many inflammatory and degenerative diseases affecting multiple organs, individually or simultaneously. Fibrosis develops when extracellular matrix (ECM) remodeling becomes excessive or uncontrolled and is associated with nearly all forms of heart disease. Cardiac fibroblasts and myofibroblasts are the main effectors of ECM deposition and scar formation. The heart is a complex multicellular organ, where the various resident cell types communicate between themselves and with cells of the blood and immune systems. Exosomes, which are small extracellular vesicles, (EVs), contribute to cell-to-cell communication and their pathophysiological relevance and therapeutic potential is emerging. Here, we will critically review the role of endogenous exosomes as possible fibrosis mediators and discuss the possibility of using stem cell-derived and/or engineered exosomes as anti-fibrotic agents

Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts

peer-reviewedBackground: The genus Lactobacillus is characterized by an extraordinary degree of phenotypic and genotypic diversity, which recent genomic analyses have further highlighted. However, the choice of species for sequencing has been non-random and unequal in distribution, with only a single representative genome from the L. salivarius clade available to date. Furthermore, there is no data to facilitate a functional genomic analysis of motility in the lactobacilli, a trait that is restricted to the L. salivarius clade. Results: The 2.06 Mb genome of the bovine isolate Lactobacillus ruminis ATCC 27782 comprises a single circular chromosome, and has a G+C content of 44.4%. In silico analysis identified 1901 coding sequences, including genes for a pediocin-like bacteriocin, a single large exopolysaccharide-related cluster, two sortase enzymes, two CRISPR loci and numerous IS elements and pseudogenes. A cluster of genes related to a putative pilin was identified, and shown to be transcribed in vitro. A high quality draft assembly of the genome of a second L. ruminis strain, ATCC 25644 isolated from humans, suggested a slightly larger genome of 2.138 Mb, that exhibited a high degree of synteny with the ATCC 27782 genome. In contrast, comparative analysis of L. ruminis and L. salivarius identified a lack of long-range synteny between these closely related species. Comparison of the L. salivarius clade core proteins with those of nine other Lactobacillus species distributed across 4 major phylogenetic groups identified the set of shared proteins, and proteins unique to each group. Conclusions: The genome of L. ruminis provides a comparative tool for directing functional analyses of other members of the L. salivarius clade, and it increases understanding of the divergence of this distinct Lactobacillus lineage from other commensal lactobacilli. The genome sequence provides a definitive resource to facilitate investigation of the genetics, biochemistry and host interactions of these motile intestinal lactobacilli

Road Transportable Analytical Laboratory system. Phase 1

This developmental effort clearly shows that a Road Transportable Analytical Laboratory System is a worthwhile and achievable goal. The RTAL is designed to fully analyze (radioanalytes, and organic and inorganic chemical analytes) 20 samples per day at the highest levels of quality assurance and quality control. It dramatically reduces the turnaround time for environmental sample analysis from 45 days (at a central commercial laboratory) to 1 day. At the same time each RTAL system will save the DOE over $12 million per year in sample analysis costs compared to the costs at a central commercial laboratory. If RTAL systems were used at the eight largest DOE facilities (at Hanford, Savannah River, Fernald, Oak Ridge, Idaho, Rocky Flats, Los Alamos, and the Nevada Test Site), the annual savings would be$96,589,000. The DOE`s internal study of sample analysis needs projects 130,000 environmental samples requiring analysis in FY 1994, clearly supporting the need for the RTAL system. The cost and time savings achievable with the RTAL system will accelerate and improve the efficiency of cleanup and remediation operations throughout the DOE complex

Bacterial Vaginosis Associated with Increased Risk of Female-to-Male HIV-1 Transmission: A Prospective Cohort Analysis among African Couples

In a prospective study, Craig Cohen and colleagues investigate the association between bacterial vaginosis and the risk of female-to-male HIV-1 transmission

Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals

peer-reviewedIn this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.Science Foundation Irelan

Platelets induce free and phospholipid-esterified 12-hydroxyeicosatetraenoic acid generation in colon cancer cells by delivering 12-lipoxygenase

Platelets promote tumor metastasis by inducing promalignant phenotypes in cancer cells and directly contributing to cancer-related throm-botic complications. Platelet-derived extracellular vesicles (EVs) can promote epithelial-mesenchymal transition (EMT) in cancer cells, which confers high-grade malignancy. 12S-hydroxyeicosatetraenoic acid (12-HETE) generated by platelet-type 12-lipoxygenase (12-LOX) is considered a key modulator of cancer metastasis through unknown mechanisms. In plate-lets, 12-HETE can be esterified into plasma membrane phospholipids (PLs), which drive thrombosis. Using cocultures of human platelets and human colon adenocarcinoma cells (line HT29) and LC-MS/MS, we investigated the impact of platelets on cancer cell biosynthesis of 12S-HETE and its esterification into PLs and whether platelet ability to transfer its mo-lecular cargo might play a role. To this aim, we performed coculture experiments with CFSE[5-(and-6)-carboxyfluorescein diacetate, succinimidyl ester]-loaded platelets. HT29 cells did not generate 12S-HETE or express 12-LOX. However, they ac-quired the capacity to produce 12S-HETE mainly esterified in plasmalogen phospholipid forms following the uptake of platelet-derived medium-sized EVs (mEVs) expressing 12-LOX. 12-LOX was detected in plasma mEV of patients with adenomas/ adenocarcinomas, implying their potential to deliver the protein to cancer cells in vivo. In cancer cells exposed to platelets, endogenous but not exogenous 12S-HETE contributed to changes in EMT gene expression, mitigated by three structurally unrelated 12-LOX inhibitors. In conclusion, we showed that platelets induce the generation of primarily esteri-fied 12-HETE in colon cancer cells following mEV-mediated delivery of 12-LOX. The modification of cancer cell phospholipids by 12-HETE may functionally impact cancer cell biology and represent a novel target for anticancer agent development