There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

http://www.klinikaikozpont.u-szeged.hu/pedia/images/pdf/CME_TEL/Full-Text/25.pdf

The Hallmarks of Aging

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

/pdf/metagenomic-biomarker-discovery-and-explanation-x530ilzkca.pdf

Metagenomic biomarker discovery and explanation

We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.

http://science.sciencemag.org/content/sci/298/5600/1912.full.pdf

The Protein Kinase Complement of the Human Genome

An expert panel was convened in October 2013 by the International Scientific Association for Probiotics and Prebiotics (ISAPP) to discuss the field of probiotics. It is now 13 years since the definition of probiotics and 12 years after guidelines were published for regulators, scientists and industry by the Food and Agriculture Organization of the United Nations and the WHO (FAO/WHO). The FAO/WHO definition of a probiotic--"live microorganisms which when administered in adequate amounts confer a health benefit on the host"--was reinforced as relevant and sufficiently accommodating for current and anticipated applications. However, inconsistencies between the FAO/WHO Expert Consultation Report and the FAO/WHO Guidelines were clarified to take into account advances in science and applications. A more precise use of the term 'probiotic' will be useful to guide clinicians and consumers in differentiating the diverse products on the market. This document represents the conclusions of the ISAPP consensus meeting on the appropriate use and scope of the term probiotic.

/pdf/expert-consensus-document-the-international-scientific-1zd5d1fmxy.pdf

Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic

The hepatic matrisome is involved in the remodeling phase of liver regeneration. As the gut microbiota has been implicated in liver regeneration, we investigated its role in liver regeneration focusing on gene expression of the hepatic matrisome after partial hepatectomy (PHx) in germ-free (GF) mice, and in GF mice reconstituted with normal gut microbiota (XGF). Liver mass restoration, hepatocyte proliferation, and immune response were assessed following 70% PHx. Hepatic matrisome and collagen gene expression were also analyzed. Reduced liver weight/body weight ratio, mitotic count, and hepatocyte proliferative index at 72 h post PHx in GF mice were preceded by reduced expression of cytokine receptor genes Tnfrsf1a and Il6ra, and Hgf gene at 3 h post PHx. In XGF mice, these indices were significantly higher than in GF mice, and similar to that of control mice, indicating normal liver regeneration. Differentially expressed genes (DEGs) of the matrisome were lower in GF compared to XGF mice at both 3 h and 72 h post PHx. GF mice also demonstrated lower collagen expression, with significantly lower expression of Col1a1, Col1a2, Col5a1, and Col6a2 compared to WT mice at 72 h post PHx. In conclusion, enhanced liver regeneration and matrisome expression in XGF mice suggests that interaction of the gut microbiota and matrisome may play a significant role in the regulation of hepatic remodeling during the regenerative process.

/pdf/impact-of-gut-recolonization-on-liver-regeneration-hepatic-1h0lh5jf.pdf

Impact of Gut Recolonization on Liver Regeneration: Hepatic Matrisome Gene Expression after Partial Hepatectomy in Mice

7 – The therapeutic use of probiotics in gastrointestinal inflammation

Intestinal Effects of Bacterial Chemotactic Peptides: Induction of Inflammation, Release of Eicosanoids.

Thrombosis, factor V Leiden, and inflammatory bowel disease

Weight loss and low body fat have been reported in adult patients with Crohn’s disease (CD). In addition, deficiencies in several nutrients have also been reported in patients with CD, but it is not clear whether these deficiencies arise as a consequence of inadequate intake and/or poor intestinal absorption and increased requirement, as a result of disease. The aim of the study was to compare dietary intakes and body composition of a group of adult patients with long-standing CD, currently in remission, with that of a group of ageand gender-matched healthy control subjects. Forty adult patients with CD (eighteen men and twenty-two women), currently in remission and with long-standing (>5 years) disease, were recruited from the Inflammatory Bowel Disease Clinic of Cork University Hospital. Remission was defined at the time of study as the absence of gastrointestinal symptoms and not requiring therapeutic doses of corticosteroids. Forty ageand gender-matched healthy control subjects were recruited from the Cork City area. Dietary intake was estimated using a 7-day diet history and analysed for nutrients using WISP (Weighted Intake Software Program) (Tinuviel Software, Warrington, UK). All statistical analysis was carried out using SPSS version 15.0 (SPSS Inc., Chicago, IL). There was a significant (P<0.01) difference in the proportion of patients with CD and healthy controls that were classified (on basis of BMI) as being underweight, normal weight, overweight or obese. There were no significant differences in waist circumference (P = 0.41), hip circumference (P = 0.63), percentage body fat (P = 0.1) mid-arm muscle area (P = 0.27), biceps (P = 0.55) and subscapular (P= 0.22) skinfold thickness measurements in either group. Skinfold thickness measurements at the supra-iliac and triceps sites were significantly (P = 0.03) and borderline significantly (P = 0.08) different respectively between patients with CD and healthy matched controls.

/pdf/dietary-intakes-and-body-composition-in-adult-patients-with-1rjirn0zch.pdf

Fergus Shanahan

Papers

Impact of Gut Recolonization on Liver Regeneration: Hepatic Matrisome Gene Expression after Partial Hepatectomy in Mice

7 – The therapeutic use of probiotics in gastrointestinal inflammation

Intestinal Effects of Bacterial Chemotactic Peptides: Induction of Inflammation, Release of Eicosanoids.

Thrombosis, factor V Leiden, and inflammatory bowel disease

Dietary intakes and body composition in adult patients with long-standing Crohn's disease currently in remission