City of Culture 2600 BC

City of culture, 2600 BC presents the city which lies beneath the surface of the archaeological site of Abu Salabikh in south Iraq, first investigated in the 1960s and excavated in the 1970s and 1980s. It starts from the facts on the ground, and shows how the material remains can resurrect the city, illuminated by its library of literary and lexical texts, and documents from institutional administration. The archaeology and the textual data reinforce each other and together convey a picture of the city and its architecture, agricultural and industrial enterprises, and social structure. These are all integrated with our wider knowledge of south Mesopotamia at this time, and with the world view given us by the rich body of Sumerian literature – myths, epics and religious texts, but also homespun secular philosophy – to create a vivid image of city life in 2600 BC.This is an account of one city and what it tells us. Cities were the defining components of early Mesopotamia, acting as the base for all economic, social, political and cultural activity. With their shared languages and traditions they belonged to a single cultural order, and as with other similar groupings of individual urban centres – whether in Greece, Italy or China – the rivalry and emulation generates a vibrant but varied and innovative world. The book concludes therefore with a more general account of “The Land” (kalam) in the pre-imperial Early Dynastic era, and with an assessment of the nature of the early Mesopotamian urban scene

Duodenal carcinoma at the ligament of Treitz. A molecular and clinical perspective

Background There is very small occurrence of adenocarcinoma in the small bowel. We present a case of primary duodenal adenocarcinoma and discuss the findings of the case diagnostic modalities, current knowledge on the molecular biology behind small bowel neoplasms and treatment options. Case The patient had a history of iron deficiency anemia and occult bleeding with extensive workup consisting of upper endoscopy, colonoscopy, capsule endoscopy, upper gastrointestinal series with small bowel follow through and push enteroscopy. Due to persistent abdominal pain and iron deficiency anemia the patient underwent push enteroscopy which revealed adenocarcinoma of the duodenum. The patient underwent en-bloc duodenectomy which revealed T3N1M0 adenocarcinoma of the 4th portion of the duodenum. Conclusions Primary duodenal carcinoma, although rare should be considered in the differential diagnosis of occult gastrointestinal bleeding when evaluation of the lower and upper GI tract is unremarkable. We discuss the current evaluation and management of this small bowel neoplasm

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

Diversity and distribution of sulphate-reducing bacteria in human faeces from healthy subjects and patients with inflammatory bowel disease

The relative abundance of different groups of sulphate-reducing bacteria (SRB) in faecal DNA collected before and after therapy from patients suffering from Crohn's disease (CD), irritable bowel syndrome (IBS) or ulcerative colitis (UC) has been compared with that from healthy controls. Growth tests revealed that SRB were not more abundant in samples from patients with CD before treatment than in the healthy control group. For most of the 128 samples available, these preliminary results were confirmed using degenerate PCR primers that amplify the dsrAB gene. However, some samples from patients with CD before treatment contained a growth inhibitor that was absent from IBS or UC samples. In-depth sequencing of PCR-generated dsrB fragments revealed that the diversity detected was surprisingly low, with only eight strains of SRB and the sulphite-reducing bacterium, Bilophila wadsworthia, detected above the 0.1% threshold. The proportion of the two major species detected, B.wadsworthia and Desulfovibrio piger, was as high as 93.5% of the total SRB population in the healthy control group and lower in all patient groups. Four previously undescribed species were found: it is impossible to predict whether they are sulphate or sulphite-reducing bacteria

Aspects of the metabolism of microorganisms

Section 1. Acetobacter suboxydans (American Type Culture Collection No. 621) is an organism of the Pseudomonas family found in spoiled beer. Among the substances it requires for growth is p-aminobenzoic acid (p-AB), and since this substance is known to prevent the inhibition of bacterial growth by sulphonamides, the inter-relations of p-AB and a sulphonamide drug in the growth of A. suboxydans were investigated. The main approach was through a study of the variations which enabled the organism (1) to grow without p-AB and (2) to resist inhibition by sulphonamides. Such changes were likely to be associated with interesting variations in the metabolism of p-AB, since there is evidence, for instance, that in certain organisms sulphonamide resistance is due to an increased ability to synthesize p-AB. For the majority of organisms p-AB overcomes sulphonamide inhibition in a competitive manner: for a given degree of inhibition the ratio of the concentrations of p-AB an sulphonamide is constant, though the absolute amounts of these may be varied considerably. Competitive relationships of this kind suggest that both metabolite and inhibitor react with the enzyme normally using the metabolite, and that the proportion of each reacting is governed by the law of mass action. As a contrast, in non-competitive relationships, a small amount of metabolite will overcome Inhibition over a wide range of concentrations of inhibitor. It is likely that a non-competitive antagonist of an inhibitor is, or readily becomes, a product of the cell's utilisation of a competitive antagonist. As a preliminary to this study it was necessary to obtain certain information about the properties of the unchanged strain of A. suboxydans, and the following points were established: The growth of the organism was very sensitive to the air supply: optimal aeration gave optical growth. The organism was normally cultured in a medium of glycerol, casein hydrolysate, vitamins and salts (Medium 2, Appendix 2), but it grew to a limited extent in a medium in which glucose replaced glycerol. The limited growth in glucose medium was probably due to rapid acid formation from this substrate. Growth in glycerol medium was also affected by addition of glucose: at low concentrations glucose stimulated growth, but at higher levels it was inhibitory. The strain used in this laboratory would not grow satisfactorily on a synthetic medium similar to that used by Stokes &amp; Larsen (1945). The organism required between 4 × 10-9 and 1.6 × 10-9 M p-AB to show visible growth in Medium 2, p-AB could be replaced by synthetic pteroylglutamic acid when added at about 100-fold greater molar concentration. Adenine replaced p-AB entirely, but not only was it required at a greater concentration than 10-5 M, but only a small stationary population of cells was reached in adenine cultures. The response to p-AB was affected by the amount of casein hydrolysate added to the medium, and certain amendments had to be made to the original medium as published by Landy &amp; Dicken (1942). The effect was not due to p-AB contained as impurity in the casein hydrolysate. Both p-AB and pteroylglutamic acid overcame sulphonamide inhibition of growth in a competitive manner. With 10-7 M p-AB the organism was able to resist between 10-4 and 2 × 10-4 M sulphathiazole. Adenine, however, acted non-competitively, permitting growth in all concentrations of drug up to 2 × 10-3 M. A synergism between pteroylglutamic acid and a mixture due to Lampen, Roepke &amp; Jones (1946) of purines, methionine and thymine was traced to the adenine in the mixture. Extracts of the organism were prepared which replaced folic acid for Lactobacillus casei and adenine for an "adenine-less" mutant of Neurospora crassa. The folic acid content of cells of A. suboxydans was independent of their age and of the amount of p-AB in which they were grown. Extracts of the kind mentioned above were used for comparison of the quantitative properties of the variant strains described below. "Sub-strains" of A. suboxydans 621 were obtained trained to dispense with p-AB (strain A) and to resist some 200 times the normal amount of sulphathiazole for a given amount of p-AB (strain C). Throughout this work sulphathiazole was used as the sulphonamide type drug in preference to sulphanilamide amide as the latter is known to effect the CO2 enzymes of cells in a manner not shown by its analogues. The sulphathiazole-resistant strain, strain C, was shown to have undergone no change in its requirement for p-AB in its normal medium. That is to say that it required the same amount of p-AB to give visible growth after a fixed time as did the parent strain, though its medium contained 2 × 10-3 M sulphathiazole. Its growth curve in a medium containing this amount of sulphathiazole and 10-7 M p-AB was similar to that of the parent strain growing in the same conditions but without sulphathiazole. On the other hand, strain C could grow in the absence of added p-AB if sulphathiazole were also omitted; the extent of growth was then limited. The relationship between p-AB and sulphathiazole in strain C was still competitive; there had merely been a change in the molar ratio of these two substances required to cause inhibition. The strain did not destroy sulphathiazole. The non-exacting strain, strain A, grew without added p-AB, but still resembled the parent organism in that it required nicotinic and pantothenic acids for growth. It had an increased resistance to sulphathiazole compared with the parent organism when both were tested with 10-7 M p-AB, though this resistance was not as great as that of strain C. The relationship between p-AB and sulphathiazole was also competitive in this strain. The growth of strain A was affected by the amount of "vitamin-free" casein hydrolysate provided in its medium: growth in Medium 2 was limited compared with the other strains. In this medium its extent of growth was increased by: p-AB Pteroylglutamic acid at some 100 times the molar concentration at which p-AB was active. High concentrations of aspartic acid. Glucose at some concentrations. Increased amounts of vitamin-free casein hydrolysate. This last effect was not shown, however, by a second strain of this type called strain A2. The stimulation of growth by casein hydrolysate was not due to the presence of p-AB in this material. Many pure vitamins, amino-acids and other compounds of importance in general cell metabolism were tested for ability to stimulate the growth of strain A; only those mentioned above were active. Other strains. An unsuccessful attempt was made to train strain A to resist sulphathiazole further by serial subculture in partially inhibitory concentrations of drug. Similarly, an attempt was made to reduce to zero the p-AB requirement of strain C in the presence of its normal concentration of sulphathiazole (2 × 10-3 M). This was also unsuccessful, though a peculiar strain (strain CD) was obtained after prolonged subculture with suboptimal amounts of p-AB. The possible synthesis of p-AB, folic acid and adenine by the trained and normal strains of A. suboxydans was investigated. Attempts to detect synthesis of p-AB by strains A and C were made by ether extraction of cultures grown without this growth factor. The extracts were concentrated and assayed with a strain of normal A. suboxydans trained to grow in the presence of the extracts. Ho synthesis of p-AB was detected. Synthesis of folic acid did occur with strain C, and the folic acid content of cells of this strain (assayed with Lb. casei) was the same as the content of cells of the parent strain. This was true of cells grown both with and without sulphathiazole. The folic acid content of cells of strain A was very much diminished compared with the other two strains. It is unlikely that any of the strains of A. suboxydans synthesised the pteroylglutamic acid molecule as such, because the shapes of the assay curves with Lb. casei using bacterial extracts were different from the control curves obtained with a sample of pteroylglutamic acid. Assays of whole cultures of A. suboxydans with Lb. casei were complicated by the presence of an inhibitor of Lb. casei in the assay material, and no conclusive results were obtained. Synthesis of adenine occurred in strains A and C as well as in the parent strain; it was detected by assay with an "adenine-less" mutant of N. crassa. The adenine content of cells of all three strains was similar, and its presence probably accounted for the non-competitive anti-sulphathiazole activity of cell extracts for the normal strain. Comparisons with Escherichia coli 273-384. This was a mutant of Esch. coli requiring p-AB for growth, and some variant strains analogous to A and C in A. suboxydans were isolated and investigated. The organism was readily trained to grow in the absence of vitamin and the resulting variant grew to the same extent as its parent growing optimally and its growth was not stimulated by p-AB. Its resistance to sulphathiazole was the same as that of its parent when both were tested with 10-7 M p-AB. A strain was obtained having a sulphathiazole resistance increased by about 50-fold for a given amount of p-AB, but its resistance was not successfully increased further. In the absence of sulphathiazole it still required p-AB for growth (unlike strain C of A. suboxydans), and in the presence of drug its requirement for p-AB was considerable. The training was in a sense incomplete, since the growth rate of the resistant organism was less than that of the parent strain even after many subcultures in the training medium. Discussion. The results outlined above were discussed in an attempt to understand further the mechanisms of the variations. that had taken place in A. suboxydans. It was considered to be unlikely that either strain had developed an ability to synthesise p-AB, though the possibility that extremely small amounts were synthesised could not be eliminated entirely. Strain A was regarded as having developed a mode of growth independent of this vitamin, and probably also of folic acid; its growth was probably dependent on the supply of amino-acids. The view was taken that, while strain C may possibly have undergone a change of the same type as that undergone by strain A, this was not the change responsible for its high sulphathiazole resistance. The primary change was considered to be a quantitative expansion of p-AB-utilising enzyme in the cell, at the surface of which p-AB and sulphonamides can be regarded as competing. An increase in affinity of the enzyme for p-AB as compared with sulphathiazole would also account for the experimental data. The point was made that further York on the rates of utilisation of p-AB, or rates of formation of products from p-AB, would be of interest. A brief mathematical consideration of this view was given to show that a roughly 80-fold expansion of p-AB-utilising enzyme would account for the 200-fold increase in sulphathiazole resistance observed. Section 2. Concurrently with the work on the variations of A. suboxydans some experiments were undertaken on the interactions of artificially induced mutants requiring p-AB for growth. In view of the results of other workers on induced mutants it is likely that mutations resulting in a growth factor requirement are due to damage to one stage in a sequence of biochemical reactions leading normally to the synthesis of the factor required. This may be represented: A → B → C → D → E → F..... → metabolite. In various organisms with a similar requirement these interruptions may well be at different stages in the sequence, and, as Beadle (1945) and his co-workers have shown with N. crassa, a mutant damaged, for example, between A and B will sometimes respond to extracts if one damaged between C and D, since C may accumulate in cultures of the latter. Ten mutant organisms requiring p-AB for growth were obtained from other laboratories and tested with this possibility in view, and interactions between the mould Ophiostoma multiannulatum 617 and two mutants of Esch. coli were recorded. Interactions between two mutants of N. crassa and A. suboxydans were shown to be due to formation of glucose by N. crassa from sucrose provided in its medium. This was formed at concentrations which stimulated the growth of A. suboxydans when fluid from a grown mould culture was added to its medium.</p