Critical evaluation of faecal microbiome preservation using metagenomic analysis

The ability to preserve microbial communities in faecal samples is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we use shotgun metagenomics to rigorously evaluate the technical and compositional reproducibility of five room temperature (RT) microbial stabilisation methods compared to the best practice of flash-freezing. These methods included RNALater, OMNIGene-GUT, a dry BBL swab, LifeGuard, and a novel method for preserving faecal samples, a Copan FLOQSwab in an active drying tube (FLOQSwab-ADT). Each method was assessed using six replicate faecal samples from five participants, totalling 180 samples. The FLOQSwab-ADT performed best for both technical and compositional reproducibility, followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. We further evaluated the FLOQSwab-ADT in an additional 239 samples across 10 individuals after storage at -20 °C, RT, and 50 °C for four weeks compared to fresh controls. The FLOQSwab-ADT maintained its performance across all temperatures, indicating this method is an excellent alternative to existing RT stabilisation methods.

Drug modification of LPS-stimulated human monocyte-derived dendritic cells

Many drugs have been reported to convert dendritic cells (DCs) into a tolerogenic phenotype in vitro. However, there is evidence that an additional stimulus, such as lipopolysaccharide (LPS), may also be necessary for tolerogenic function in vivo. Little is known concerning the effects of drug modification on LPS-prestimulated DCs. In this study, monocyte-derived immature DCs were stimulated with LPS first and the influence investigated of six different agents on surface antigen expression, cytokine production and lymphocyte proliferation and cytotoxicity. Mycophenolic acid- and rapamycin-exposed DCs had little effect on surface antigen expression or functional activity towards lymphocytes. In contrast, treatment of immature dendritic cells with aspirin, dexamethasone, 1alpha,25-dihydroxyvitamin D3 (VD3) or butyric acid was associated with diminished expression of CD1a, CD1c, CD40, CD80 and CD83. Dendritic cell modification by aspirin, dexamethasone and VD3 were all associated with decreased production of tumour necrosis factor-alpha (TNFalpha). Furthermore, VD3 treatment was associated with a consistent and significant elevation of IL-6 production. Aspirin-, dexamethasone- VD3- and butyric acid-modified DCs suppressed interferon-gamma production, proliferation and cytotoxicity in co-culture with allogeneic mononuclear cells, but inconsistent results were obtained with different allogeneic combinations. Different drugs show varying effects on DC phenotype. No single agent was consistently effective in suppressing the stimulation of allogeneic mononuclear cells and future work is needed to explore drug combinations.

Association between mannan-binding lectin and impaired lung function in cystic fibrosis may be age-dependent

An association between mannan-binding lectin (MBL) status and severity of lung function impairment in cystic fibrosis (CF) has been found in several studies, but not in others. To explore the possible basis for discrepancies in the literature, we related both MBL and L-ficolin concentrations to lung function and examined the results in relation to the age of the patients. For patients under 15 years of age, those with MBL < 200 ng/ml had better lung function than those with MBL > 200 ng/ml [median forced expiratory volume in 1 s (FEV(1)), 99% versus 83%; P = 0.05]. For patients over 15 years of age, those with MBL < 200 ng/ml had poorer lung function than those with MBL > 200 ng/ml (median FEV(1), 44% versus 55%; P = 0.1). Also, for the over 15-year-olds, the proportion of patients with FEV(1) values below the median was greater in the MBL-insufficient subgroup (P < 0.04). In other words, relative deficiency of MBL appears to accelerate the age-related decline in lung function in CF patients. No corresponding relationships could be found between L-ficolin concentration and lung function. These findings and interpretation lend support to the potential value of MBL replacement therapy in a small minority of cystic fibrosis patients.

Detection of an Autologous Ligand for Mannan-Binding Lectin on Human B Lymphocytes

Mannan-binding lectin (MBL) is a collectin and a major soluble pattern-recognition protein. MBL can distinguish self from nonself and altered self using its C-type carbohydrate recognition domain and may also interact via its collagen-like region with autologous cells. Recently, it was found that MBL could bind to adherent cells (monocytes) and dendritic cells in a specific and sugar-sensitive manner. We have now investigated the interaction of MBL with fresh human peripheral blood cells and report binding to B lymphocytes and natural killer cells. The binding to B lymphocytes was studied in detail and was compared with the binding of MBL to monocytes and dendritic cells. Binding of MBL to B cells was evident at physiological MBL and calcium concentrations but was optimal at supraphysiological MBL concentrations. It was readily inhibited by autologous serum, mannan, mannose, GlcNAc and (to a lesser extent) galactose but not by C1q. A similar, but not identical, inhibition profile was observed with dendritic cells, but monocytes were not sensitive to mannose or mannan. We conclude that MBL is capable of binding to differently glycosylated ligands on several autologous cell types via its carbohydrate-recognition domain. We speculate that this could have functional significance at extravascular sites, but perhaps only in individuals possessing MBL genotypes conferring MBL sufficiency.

Nonspecific interstitial pneumonia and usual interstitial pneumonia: comparative appearances at and diagnostic accuracy of thin-section CT

PURPOSE

To compare the morphologic abnormalities on thin-section computed tomographic (CT) images in a group of patients with histopathologically confirmed nonspecific interstitial pneumonia (NSIP) or usual interstitial pneumonia (UIP) and a clinical presentation of idiopathic pulmonary fibrosis.

MATERIALS AND METHODS

Thin-section CT imaging patterns and distribution of disease in 53 patients with histologic diagnoses of NSIP (n = 21) or UIP (n = 32) were quantified retrospectively and independently by four observers. The appearances of NSIP and UIP at CT were compared with univariate and multivariate techniques.

RESULTS

The use of thin-section CT proved to have moderate sensitivity (70%), specificity (63%), and accuracy (66%) in the diagnosis of NSIP. An increased proportion of ground-glass attenuation was the cardinal feature of NSIP at CT (odds ratio: 1.04 for each 1% increase in the proportion of ground-glass attenuation). A histologic diagnosis of NSIP was most frequent (in 24 of 35 observations [69%]) when ground-glass attenuation predominated, and was more frequent with mixed (35 of 79 observations [44%]) than with predominantly reticular disease (25 of 98 [26%] observations, P < .005). Logistic regression analysis of the data indicated that misdiagnosis of UIP in patients with NSIP was associated with less ground-glass attenuation (P < .005) at CT and a subpleural disease distribution (P = .02), with the converse being true for UIP cases misdiagnosed as NSIP.

CONCLUSION

In patients with a clinical presentation of idiopathic pulmonary fibrosis, the accuracy of thin-section CT in identifying NSIP is considerably higher than previously reported. At CT, NSIP is characterized by more ground-glass attenuation and a finer reticular pattern than is UIP. Nevertheless, considerable overlap in thin-section CT patterns exists between NSIP and UIP.

Virus removal from bioproducts using ultrafiltration membranes modified with latex particle pretreatment

Ultrafiltration is an attractive process for virus removal from bioproducts owing to its high throughput as well as the fact that the operation is carried out under ambient conditions (damage to proteins is highly limited). The principal concern regarding the adoption of conventional ultrafiltration membranes for virus removal is the possibility of the virus passing through abnormally large pores or surface imperfections on the membrane surface. The chief principle behind the present work is to pretreat the membrane by blocking the abnormally large pores using latex particles. Experimental work was conducted to validate this pretreatment using the bacteriophage phi x 174 as a model virus. The results attained were highly encouraging. Different sizes of latex particles were tested by treating a 100 KD molecular weight cut-off membrane, and the transmission of phage (suspended in buffer) through this membrane assessed. In the absence of any particle pretreatment, a virus clearance of 4.78 log reduction value was observed for this membrane. The transmission of phage through the membrane could be reduced by an order of magnitude using 0.11 micron latex particles, or two orders of magnitude using a combination of 0.11 and 0.50 micron particles. The application of latex particles did not hinder the transport of protein through the 100 KD membrane. Protein sieving coefficients obtained using this membrane were 91%, 16% and 2%, for lysozyme, HSA and IgG, respectively.

Caries prevalence in xerostomic individuals

Saliva, via its lubricating, cleansing, remineralizing, antibacterial, and buffering actions, is an important protective factor for both dentition and soft tissue. Xerostomia is commonly found in older individuals due to the use of medications or medical conditions, such as Sjögren's, which directly affect salivary gland function. A xerostomic subgroup (n = 60), mean age = 60, 66 per cent female) of the Nutrition and Oral Health Study (n = 370) was reexamined for caries. Unstimulated and two-per-cent citric-acid stimulated parotid and submandibular/sublingual salivary flow rates were determined. This group was matched for number of teeth, age, sex, and alcohol and smoking habits with a medication-free subgroup (n = 60). Active root and coronal caries were found to be significantly higher in the xerostomic subgroup than in a matched subgroup of medication-free individuals. The mean DFS for the xerostomic subgroup was 45.4 +/- 21.7 for coronal caries and 5.3 +/- 5.8 for root caries. The mean number of teeth was 21.8. The mean DFS in the medication-free subgroup was 36.5 +/- 22.1 for coronal caries and 3.2 +/- 3.2 for root caries. The mean DFS in the xerostomic subgroup for coronal and root caries was statistically significantly higher (p < 0.05). The odds ratio was 2.89 for coronal caries and 3.27 for root caries in the xerostomic versus the medication-free subgroup. Caries varied inversely with salivary flow rate. The difference in flow rates for those in the lowest and highest quartile for coronal caries experience (DFS) in the xerostomic subgroup was found to be statistically significant (p < 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)

Hypotensive effects of stroma-free haemoglobin solutions attributable to adenine nucleotides

Aqueous solutions of stroma-free human haemoglobin are being evaluated as potential oxygen-carrying resuscitation fluids. There are indications, however, that such solutions may produce toxic side-effects in vivo. Stroma-free haemoglobin solution produced a 50% fall in mean arterial pressure when infused into a small animal model despite containing very low levels of non-haem protein and phospholipid contaminants. This effect was not produced by haemoglobin solutions after extensive dialysis. Red cell-derived adenine nucleotides were found to be present in concentrations high enough to cause such a response (80-85 micrograms/ml). We have developed a chromatographic assay capable of predicting hypotension in our animal model and consider that the complete absence of adenine nucleotides must be confirmed in all studies concerning the possible toxic side-effects of stroma-free haemoglobin solutions.

Statistical clustering procedures applied to low-cost speech recognition

A new generation of low-cost speech recognition devices are appearing, which offer much promise for useful applications in biomedical engineering. These devices are statistical pattern recognizers. Input utterances are classified by comparison with a set of templates derived during 'speaker training'. For useful application of these devices, recognition accuracy must be high and speaker training must not be unacceptably complicated or tedious. This paper investigates techniques which consider the statistical nature of the input utterances, used to improve recognition accuracy. Word classification based on the Mahalonobis distance metric, and using templates derived from cluster analysis of the training inputs, was found to give results superior to the other strategies studied. This classifier was unsuitable for implementation in a real-time, low-cost system but the principle of clustering was successfully applied to produce an adaptive system which tracked changes in the user's voice. This allowed training to be drastically simplified by updating templates during normal operation. The adaptive system achieved 98.8% recognition accuracy on a 32 word vocabulary compared to 94.8% without adaptation.