Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing

With the advent of high through-put sequencing (HTS), the emerging science of metagenomics is transforming our understanding of the relationships of microbial communities with their environments. While metagenomics aims to catalogue the genes present in a sample through assessing which genes are actively expressed, metatranscriptomics can provide a mechanistic understanding of community inter-relationships. To achieve these goals, several challenges need to be addressed from sample preparation to sequence processing, statistical analysis and functional annotation. Here we use an inbred non-obese diabetic (NOD) mouse model in which germ-free animals were colonized with a defined mixture of eight commensal bacteria, to explore methods of RNA extraction and to develop a pipeline for the generation and analysis of metatranscriptomic data. Applying the Illumina HTS platform, we sequenced 12 NOD cecal samples prepared using multiple RNA-extraction protocols. The absence of a complete set of reference genomes necessitated a peptide-based search strategy. Up to 16% of sequence reads could be matched to a known bacterial gene. Phylogenetic analysis of the mapped ORFs revealed a distribution consistent with ribosomal RNA, the majority from Bacteroides or Clostridium species. To place these HTS data within a systems context, we mapped the relative abundance of corresponding Escherichia coli homologs onto metabolic and protein-protein interaction networks. These maps identified bacterial processes with components that were well-represented in the datasets. In summary this study highlights the potential of exploiting the economy of HTS platforms for metatranscriptomics.

Catheter-based treatment of ilio-femoral deep vein thrombosis - an update on current evidence

Ilio-femoral deep vein thrombosis (DVT) has a high rate of long-term morbidity in the form of the postthrombotic syndrome (PTS). Therefore, management of acute thrombosis should not only focus on the prevention of acute complications such as propagation or embolisation of the initial clot but also on preventing PTS and recurrent thrombosis. Contemporary catheter-based treatments of deep vein thrombosis have proven to be safe and effective in selected patients. Current guidelines recommend medical therapy with anticoagulation alone for all but the most severe, limb-threatening thrombosis. They additionally allow for consideration of catheter-based treatment in patients with acute DVT and low risk of bleeding complications to prevent PTS. Recent studies favoring interventional therapy have not been included in these guidelines. Data on long-term outcome is expected to be published soon, clarifying and very likely strengthening the role of catheter-based treatments in the management of acute ilio-femoral DVT.

Superselective embolization of deep femoral artery branch pseudoaneurysm with a coaxial microcatheter system

This report describes the use of transluminal coil embolization to treat pseudoaneurysm of deep femoral artery branch in two patients. The pseudoaneurysms had developed after coronary angiographv in one patient and after hip replacement in the other. Immediate control angiography after embolization procedures demonstrated complete closure of the pseudoaneurysms. During follow-up of 19 and 3 months, respectively, there was no recurrent bleeding. The aim of this case report is to show the advances in endovascular microcatheter technology, and embolic materials, that made percutaneous transluminal embolization of arterial pseudoaneurysms safe and efficient. In addition, it keeps the medical personnel aware of vascular injuries at the access site related to endovascular procedures as well as vascular complications of total hip arthroplasty. It calls their attention to the possibility of endovascular treatment as an alternative to surgery.

Lymphatic clearance of the human skin in patients with acute deep vein thrombosis using a novel fluorescent technique

The purpose of this study was to investigate lymphatic clearance of the human skin in patients with acute deep thrombosis of the femoral vein. In 13 patients with deep vein thrombosis and no other cause for swelling of the limbs, lymphatic clearance of the skin at the foot was measured. Ten microliters of fluorescein isothiocyanatedextran 150,000 were injected intradermally and the fluorescent light intensity of the deposit measured 10 min and 24 hours after injection by window densitometry. In addition, intralymphatic pressure was measured by the servo-nulling system. The results were compared with a sex- and age-matched control group. Fluorescent light intensity decreased by 23.8 +/- 12.3 arbitrary units or by a factor of 1.8 +/- 0.5 in patients with DVT after 24 hours, which was significantly less than in healthy controls (33.7 +/- 8.9 arbitrary units or by factor 5.0 +/- 4.1, p < 0.013). Intralymphatic pressure was not different between the two groups. These results indicate that lymphatic clearance is significantly reduced in the acute phase of deep venous thrombosis.

Curing capability of halogen and LED light curing units in deep class II cavities in extracted human molars

Class II cavities were prepared in extracted lower molars filled and cured in three 2-mm increments using a metal matrix. Three composites (Spectrum TPH A4, Ceram X mono M7 and Tetric Ceram A4) were cured with both the SmartLite PS LED LCU and the Spectrum 800 continuous cure halogen LCU using curing cycles of 10, 20 and 40 seconds. Each increment was cured before adding the next. After a seven-day incubation period, the composite specimens were removed from the teeth, embedded in self-curing resin and ground to half the orofacial width. Knoop microhardness was determined 100, 200, 500, 1000, 1500, 2500, 3500, 4500 and 5500 microm from the occlusal surface at a distance of 150 microm and 1000 microm from the metal matrix. The total degree of polymerization of a composite specimen for any given curing time and curing light was determined by calculating the area under the hardness curve. Hardness values 150 microm from the metal matrix never reached maximum values and were generally lower than those 1000 microm from the matrix. The hardest composite was usually encountered between 200 microm and 1000 microm from the occlusal surface. For every composite-curing time combination, there was an increase in microhardness at the top of each increment (measurements at 500, 2500 and 4500 microm) and a decrease towards the bottom of each increment (measurements at 1500, 3500 and 5500 microm). Longer curing times were usually combined with harder composite samples. Spectrum TPH composite was the only composite showing a satisfactory degree of polymerization for all three curing times and both LCUs. Multiple linear regression showed that only the curing time (p < 0.001) and composite material (p < 0.001) had a significant association with the degree of polymerization. The degree of polymerization achieved by the LED LCU was not significantly different from that achieved by the halogen LCU (p = 0.54).

An in vivo study of a growth-factor enhanced, cell free, two-layered collagen-tricalcium phosphate in deep osteochondral defects

Focal osteochondral defects are still a challenging problem in joint surgery. We have developed a two-layered implant consisting of a basal porous beta-tricalcium phosphate (TCP) for bone reconstruction and a superficial fibrous collagen type I/III layer for cartilage regeneration. Fifty-four osteochondral defects in the trochlear groove of 27 Göttinger Minipigs were created and either left untreated, treated with the implant alone, or the implant augmented with an additional growth factor mixture, which was assumed to stimulate cell and tissue differentiation. Follow-up was 6, 12 and 52 weeks with n=6 for each group. The repair tissue was evaluated for its gross appearance and biomechanical properties. Histological sections were semi-quantitatively scored for their histomorphological structure. Treatment with the two-layered implant improved defect filling and subchondral bone repair at 6 and 12 weeks follow-up. The TCP was replaced by cancellous bone at 52 weeks. Cartilage repair tissue mainly consisted of fibrocartilage and showed a moderate cell density up to the joint surface. Growth factor treatment improved the mechanical and histomorphological properties of the cartilage repair tissue at 12, but not at 52 weeks postoperatively. In conclusion, the two-layered collagen-TCP implant augmented with chondroinductive growth factors seems a promising new option for the treatment of deep osteochondral defects in joint surgery.

Real-time quantitative broad-range PCR assay for detection of the 16S rRNA gene followed by sequencing for species identification

Here we determined the analytical sensitivities of broad-range real-time PCR-based assays employing one of three different genomic DNA extraction protocols in combination with one of three different primer pairs targeting the 16S rRNA gene to detect a panel of 22 bacterial species. DNA extraction protocol III, using lysozyme, lysostaphin, and proteinase K, followed by PCR with the primer pair Bak11W/Bak2, giving amplicons of 796 bp in length, showed the best overall sensitivity, detecting DNA of 82% of the strains investigated at concentrations of < or =10(2) CFU in water per reaction. DNA extraction protocols I and II, using less enzyme treatment, combined with other primer pairs giving shorter amplicons of 466 bp and 342 or 346 bp, respectively, were slightly more sensitive for the detection of gram-negative but less sensitive for the detection of gram-positive bacteria. The obstacle of detecting background DNA in blood samples spiked with bacteria was circumvented by introducing a broad-range hybridization probe, and this preserved the minimal detection limits observed in samples devoid of blood. Finally, sequencing of the amplicons generated using the primer pair Bak11W/Bak2 allowed species identification of the detected bacterial DNA. Thus, broad-spectrum PCR targeting the 16S rRNA gene in the quantitative real-time format can achieve an analytical sensitivity of 1 to 10 CFU per reaction in water, avoid detection of background DNA with the introduction of a broad-range probe, and generate amplicons that allow species identification of the detected bacterial DNA by sequencing. These prerequisites are important for its application to blood-containing patient samples.