Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis

Aim: The aim of this study was to characterize the bacterial community adhering to the mucosa of the terminal ileum, and proximal and distal colon of the human digestive tract. Methods and Results: Pinch samples of the terminal ileum, proximal and distal colon were taken from a healthy 35-year-old, and a 68-year-old subject with mild diverticulosis. The 16S rDNA genes were amplified using a low number of PCR cycles, cloned, and sequenced. In total, 361 sequences were obtained comprising 70 operational taxonomic units (OTU), with a calculated coverage of 82.6%. Twenty-three per cent of OTU were common to the terminal ileum, proximal colon and distal colon, but 14% OTU were only found in the terminal ileum, and 43% were only associated with the proximal or distal colon. The most frequently represented clones were from the Clostridium group XIVa (24.7%), and the Bacteroidetes (Cytophaga-Flavobacteria-Bacteroides ) cluster (27.7%). Conclusion: Comparison of 16S rDNA clone libraries of the hindgut across mammalian species confirms that the distribution of phylogenetic groups is similar irrespective of the host species. Lesser site-related differences within groups or clusters of organisms, are probable. Significance and Impact: This study provides further evidence of the distribution of the bacteria on the mucosal surfaces of the human hindgut. Data contribute to the benchmarking of the microbial composition of the human digestive tract.

Economic competition and evolution: Are there lessons from ecology?

After generally discussing models in ecology and economics that combine competition, optimization, and evolution, this article concentrates on models of intraspecific competition. It demonstrates the importance of diversity/inequalities within populations of species and other environments for the sustainability of their populations, given the occurrence of environmental change. This is demonstrated both for scramble (open-access) and contest competition. Implications are drawn for human populations and industrial organization. The possibility is raised that within-industry competition may not always exist between firms in all stages of the development of a new industry. Policy implications are considered. For example, it is argued that policies designed to encourage intense business competition and maximum economic efficiency have the drawback of eventually making industries highly vulnerable to exogenous economic changes.

Human behaviour modelled as a statistico-deterministic turing machine

'Free will' and its corollary, the concept of individual responsibility are keystones of the justice system. This paper shows that if we accept a physics that disallows time reversal, the concept of 'free will' is undermined by an integrated understanding of the influence of genetics and environment on human behavioural responses. Analysis is undertaken by modelling life as a novel statistico-deterministic version of a Turing machine, i.e. as a series of transitions between states at successive instants of time. Using this model it is proven by induction that the entire course of life is independent of the action of free will. Although determined by prior state, the probability of transitions between states in response to a standard environmental stimulus is not equal to 1 and the transitions may differ quantitatively at the molecular level and qualitatively at the level of the whole organism. Transitions between states correspond to behaviours. It is shown that the behaviour of identical twins (or clones), although determined, would be incompletely predictable and non-identical, creating an illusion of the operation of 'free will'. 'Free will' is a convenient construct for current judicial systems and social control because it allows rationalization of punishment for those whose behaviour falls outside socially defined norms. Indeed, it is conceivable that maintenance of ideas of free will has co-evolved with community morality to reinforce its operation. If the concept is free will is to be maintained it would require revision of our current physical theories.

Microarray and proteomic analysis of the human alcoholic brain

The superior frontal cortex (SFC) is selectively damaged in chronic alcohol abuse, with localized neuronal loss and tissue atrophy. Regions such as motor cortex show little neuronal loss except in severe co-morbidity (liver cirrhosis or WKS). Altered gene expression was found in microarray comparisons of alcoholic and control SFC samples [1]. We used Western blots and proteomic analysis to identify the proteins that also show differential expression. Tissue was obtained at autopsy under informed, written consent from uncomplicated alcoholics and age- and sex-matched controls. Alcoholics had consumed 80 g ethanol/day chronically (often, 200 g/day for 20 y). Controls either abstained or were social drinkers ( 20 g/day). All subjects had pathological confirmation of liver and brain diagnosis; none had been polydrug abusers. Samples were homogenized in water and clarified by brief centrifugation (1000g, 3 min) before storage at –80°C. For proteomics the thawed suspensions were centrifuged (15000g, 50 min) to prepare soluble fractions. Aliquots were pooled from SFC samples from the 5 chronic alcoholics and 5 matched controls used in the previous microarray study [1]. 2-Dimensional electrophoresis was performed in triplicate using 18 cm format pH 4–7 and pH 6–11 immobilized pH gradients for firstdimension isoelectric focusing. Following second-dimension SDS-PAGE the proteins were fluorescently stained and the images collected by densitometry. 182 proteins differed by 2-fold between cases and controls. 141 showed lower expression in alcoholics, 33 higher, and 8 were new or had disappeared. To date 63 proteins have been identified using MALDI-MS and MS-MS. Western blots were performed on uncentrifuged individual samples from 76 subjects (controls, uncomplicated alcoholics and cirrhotic alcoholics). A common standard was run on every gel. After transfer, immunolabeling, and densitometry, the intensities of the unknown bands were compared to those of the standards. We focused on proteins from transcripts that showed clear differences in a series of microarray studies, classified into common sets including Regulators of G-protein Signaling and Myelin-associated proteins. The preponderantly lower level of differentially expressed proteins in alcoholics parallels the microarray mRNA analysis in the same samples. We found that mRNA and protein expression do not frequently correspond; this may help identify pathogenic processes acting at the level of transcription, translation, or post-translationally.