Diversity of the trifunctional histidine biosynthesis gene (his) in cereal Phaeosphaeria species.

Phaeosphaeria species are important causal agents of Stagonospora leaf blotch diseases in cereals. In this study, the nucleotide sequence and deduced polypeptide of the trifunctional histidine biosynthesis gene (his) are used to investigate the phylogenetic relationships and provide molecular identification among cereal Phaeosphaeria species. The full-length sequences of the his gene were obtained by PCR amplification and compared among cereal Phaeosphaeria species. The coding sequence of the his gene in wheat-biotype P. nodorum (PN-w) was 2697 bp. The his genes in barley-biotype P. nodorum (PN-b), two P. avenaria f. sp. triticea isolates (homothallic Pat1 and Pat3), and Phaeosphaeria species from Polish rye and dallis grass were 2694 bp. The his gene in heterothallic isolate Pat2, however, was 2693 bp because the intron had one fewer base. In P. avenaria f. sp. avenaria (Paa), the his gene was only 2670 bp long. The differences in the size of the his gene contributed to the variation in amino acid sequences in the gap region located between the phosphoribosyl-ATP pyrophosphohydrolase and histidinol dehydrogenase sub-domains. Based on nucleotide and deduced amino acid sequences of the his gene, Pat1 was not closely related to either PN-w or the Paa clade. It appears that rates of evolution of the his gene were fast in cereal Phaeosphaeria species. The possible involvement of meiotic recombination in genetic diversity of the his gene in P. nodorum is discussed.     

Mutation spoT of Escherichia coli increases expression of the histidine operon deleted for the attenuator.

F'-episomes carrying the Salmonella typhimurium wild-type or attenuator-deleted histidine (his) operons were introduced into Escherichia coli strains containing relA or spoT single and double mutations known to affect guanosine 3'-diphosphate 5'-diphosphate (ppGpp) and guanosine 3'-triphosphate 5'-diphosphate (pppGpp) levels. Expression of the his operon and expression of the gene for 6-phosphogluconate dehydrogenase (gnd) were measured during balanced growth in amino acid-rich and minimal media. The data were consistent with the interpretation that ppGpp is a positive effector of his operon expression, whereas pppGpp is not an essential effector. The conclusion that his operon expression is maximally stimulated at a lower than maximum intracellular ppGpp concentration was further confirmed. Neither ppGpp nor pppGpp appeared to influence gnd gene expression. The metabolic regulation of the E. coli his operon was found to be similar to the ppGpp-meidated metabolic regulation of the S. typhimurium his operon.     

Comparison of Deoxyribonucleic Acid Uptake and Marker Integration in Bacilli and Protoplasts of Bacillus subtilis

trp(+)his(-) donor deoxyribonucleic acid (DNA) was added to highly competent trp(-)his(+) recipient bacilli and to protoplasts prepared from these bacilli, and the cell-DNA complexes were incubated for 30 min. The complexes were then washed and lysed, and their DNA was analyzed on a trp(-)his(-) strain for the donor marker trp(+), the resident marker his(+), and for the recombinant trp(+)his(+) combination. The extracts of the bacillary complexes contained a normal percentage of donor markers (0.1-0.2%), and the number of trp(+)his(+) doubles (20% of all trp(+) transformants) indicated that the donor DNA had become integrated into the resident genomes. The protoplast complexes contained 10 to 1,000 times fewer donor markers and almost no recombinants. This indicated that, in protoplasts, marker uptake was minimal and recombination was absent. Uptake was also measured with (3)H-labeled DNA. On the average, protoplasts took up one-fiftieth as much DNA as bacilli. It was concluded that, probably, protoplasts took up no DNA at all, that there were no DNA affinity sites on the surface of the protoplasts, and that the residual marker and radioactivity uptake was due to imperfections in the experimental system. The data and conclusions differed sharply from earlier ones of Hirokawa and Ikeda despite the fact that the techniques of these authors were followed in repeat experiments.     

Who was... Almroth Wright?

Sir Almroth Edward Wright CB MD FRS (1861-1947) was Britains first academic immunologist. He was qualified in both Arts and Medicine and commenced his professional life as a Physiologist, became Professor of Pathology and led the study of immunity to infectious diseases. He was often a controversial scientist and not always right in his views, hence his nickname 'Sir Almost Right'!     

Rethinking Woodger’s Legacy in the Philosophy of Biology

The writings of Joseph Henry Woodger (1894–1981) are often taken to exemplify everything that was wrongheaded, misguided, and just plain wrong with early twentieth-century philosophy of biology. Over the years, commentators have said of Woodger: (a) that he was a fervent logical empiricist who tried to impose the explanatory gold standards of physics onto biology, (b) that his philosophical work was completely disconnected from biological science, (c) that he possessed no scientific or philosophical credentials, and (d) that his work was disparaged – if not altogether ignored – by the biologists and philosophers of his era. In this paper, we provide the first systematic examination of Woodger’s oeuvre, and use it to demonstrate that the four preceding claims are false. We argue that Woodger’s ideas have exerted an important influence on biology and philosophy, and submit that the current consensus on his legacy stems from a highly selective reading of his works. By rehabilitating Woodger, we hope to show that there is no good reason to continue to disregard the numerous contributions to the philosophy of biology produced in the decades prior to the professionalization of the discipline.     

Challenges and opportunities for biogeography—What can we still learn from von Humboldt?

Alexander von Humboldt was arguably the most influential scientist of his day. Although his fame has since lessened relative to some of his contemporaries, we argue that his influence remains strong—mainly because his approach to science inspired others and was instrumental in furthering other scientific disciplines (such as evolution, through Darwin, and conservation science, through Muir)—and that he changed the way that large areas of science are done and communicated. Indeed, he has been called the father of a range of fields, including environmental science, earth system science, plant geography, ecology and conservation. His approach was characterized by making connections between non‐living and living nature (including humans), based on interdisciplinary thinking and informed by large amounts of data from systematic, accurate measurements in a geographical framework. Although his approach largely lacked an evolutionary perspective, he was fundamental to creating the circumstances for Darwin and Wallace to advance evolutionary science. He devoted considerable effort illustrating, communicating and popularizing science, centred on the excitement of pure science. In biogeography, his influence remains strong, including in relating climate to species distributions (e.g. biomes and latitudinal and elevational gradients) and in the use of remote sensing and species distribution modelling in macroecology. However, some key aspects of his approach have faded, particularly as science fragmented into specific disciplines and became more reductionist. We argue that asking questions in a more Humboldtian way is important for addressing current global challenges. This is well‐exemplified by researching links between geodiversity and biodiversity. Progress on this can be made by (a) systematic data collection to improve our knowledge of biodiversity and geodiversity around the world; (b) improving our understanding of the linkages between biodiversity and geodiversity; and (c) developing our understanding of the interactions of geological, biological, ecological, environmental and evolutionary processes in biogeography.     

pMB9 plasmids bearing the Salmonella typhimurium his operon and gnd gene

A plasmid containing the entire Salmonella typhimurium his operon was constructed from plasmid pM89 and an EcoRI fragment of phi 80 his imm lambda DNA. The recombinant pST41 also includes the glucose 6-phosphate dehydrogenase (gnd) gene and has one EcoRI endonuclease cleavage site in the integrated fragment. This plasmid served as a source for the construction of two additional plasmids, one carrying the OGDC-region of the his operon and the other a CBHAFIE segment of the his gene along with the gnd gene. The presence of the his operon in the constructed plasmids was confirmed by hybridization to S. typhimurium his RNA. The location of the gnd gene in the CBHAFIE fragment of the his gene was confirmed genetically: after transfection with the plasmid bearing the gnd gene, a gnd recipient gained the capacity to utilize gluconate as a sole carbon source. The DNAs of the three hybrid plasmids were analyzed by gel electrophoresis. By comparing the EcoRI endonuclease cleavage pattern of these three hybrid plasmids with the DNA cleavage pattern of phi 80 his imm lambda, phi 80 imm lambda and lambda phages, the EcoRI cleavage map of phi 80 his imm lambda was obtained.     

Scientific research at the Laboratoire Arago (Banyuls, France) in the twentieth Century: Edouard Chatton, the "master", and André Lwoff, the "pupil"

Edouard Chatton (1883–1947) began his scientific career in the Pasteur Institute, where he made several important discoveries regarding pathogenic protists (trypanosomids, Plasmodium, toxoplasms, Leishmania). In 1908 he married a "Banyulencque", Marie Herre; from 1920, he focused his research on marine protists. He finished his career as Professor at the Sorbonne (Paris) and director of the Laboratoire Arago in Banyuls-sur-mer, where he died in 1947. André Lwoff (1902–1994) lived several scientific lives in addition to his artistic and family life. But it is the study of protists that filled his first life after he encountered the exceptional Master who was Chatton. Lwoff's father was a psychiatrist and his mother an artist sculptor. He became a Doctor of Medicine in 1927 and then a Doctor of Sciences in 1932, his thesis dealing with biochemical aspects of protozoa nutrition. He met Chatton in 1921 and – until Chatton's death – their meetings, first in Roscoff and then in Banyuls-sur-mer, were numerous and their collaboration very close. Their monograph on apostome ciliates was one of the peaks of this collaboration. In 1938, Lwoff was made director of the Microbial Physiology Department at the Pasteur Institute in Paris, where he began a new life devoted to bacteria, and then to viruses, before pursuing his career as director of the Cancer Research Institute in Villejuif (France). Lwoff was awarded the Nobel Prize in Physiology or Medicine in 1965. He died in Banyuls in 1994. "Master" and "pupil" had in common perseverance in their scientific work, conception and observation, a critical sense and rigor but also a great artistic sensibility that painting and drawing in the exceptional surroundings of Banyuls-sur-mer had fulfilled. Electronic Publication     

An expression vector tailored for large-scale, high-throughput purification of recombinant proteins

Production of milligram quantities of numerous proteins for structural and functional studies requires an efficient purification pipeline. We found that the dual tag, his(6)-tag-maltose-binding protein (MBP), intended to facilitate purification and enhance proteins' solubility, disrupted such a pipeline, requiring additional screening and purification steps. Not all proteins rendered soluble by fusion to MBP remained soluble after its proteolytic removal, and in those cases where the protein remained soluble, standard purification protocols failed to remove completely the stoichiometric amount of his(6)-tagged MBP generated by proteolysis. Both liabilities were alleviated by construction of a vector that produces fusion proteins in which MBP, the his(6)-tag and the target protein are separated by highly specific protease cleavage sites in the configuration MBP-site-his(6)-site-protein. In vivo cleavage at the first site by co-expressed protease generated untagged MBP and his(6)-tagged target protein. Proteins not truly rendered soluble by transient association with MBP precipitated, and untagged MBP was easily separated from the his-tagged target protein by conventional protocols. The second protease cleavage site allowed removal of the his(6)-tag.     

Linnaeus's natural and artificial arrangements of plants

Linnaeus's artificial and natural arrangements of plants are examined using a Spearman rank coefficient (which is explained) on his presentations of his own and others' arrangements in the Classes plantarum and elsewhere. There is little alteration in his successive artificial arrangements. In contrast, between 1751 and 1764 his natural arrangements changed considerably, partly in the sequences of genera within orders but mostly by rearrangement of the orders. Comparison with Cesalpino's and Ray's natural arrangements, using the longest-recognized natural groups as signposts, suggests that Linnaeus in his latest natural arrangement (1764) approximated more closely to Ray's. Examination of Linnaeus's successive treatments of certain groups (palms, Zingiberaceae, Hydrocharis-Stratiotes-Vallisneria) and of Giseke's exposition of Linnaeus's lectures on natural groups (1792) shows that Linnaeus was much influenced by habitus and vegetative characters as well as those of the fructification. He recognized orders consisting of a chain of genera linked successively by overall affinity and without any single diagnostic character. Where possible, he preferred characters of the fructification and his ‘secret’ consulting of the habitus is explained as secondary to such characters. It is suggested that in his latest arrangement he approximated more to a scala naturae, as he probably did in zoology about the same time. Within his artificial arrangements Linnaeus kept to sequences of genera as natural as possible. He realized that some groups in his natural arrangements were still artificial, and his aphorism that all genera and species are natural, classes and orders part natural and part artificial, refers to his and others' practice until the natural system could be completed. It is not a statement of the essential natures of these ranks. Linnaeus's distinction in practice between natural and artificial arrangements was less clear-cut than Sachs believed. Linnaeus's rejection of the ancient tree/herb division was empirical, not a reasoned repudiation of an a priori grouping. The tree/herb division could be upheld in his day as obviously natural, not merely accepted on authority.     

Aptamers as detection molecules on reverse phase protein microarrays for the analysis of cell lysates

This study presents and discusses the application of Cy3‐labeled aptamers (where Cy3 is indocarbocyanine) directed against the his‐tag (where his is histidine) for the detection of his‐tagged proteins on microarrays in a so‐called reverse phase assay. These types of assays are widely used tools in protein microarray technology. Up to now antibodies are usually applied as detection molecules. Here, two different spotting techniques, contact and noncontact spotting, as well as different types of slides, aldehyde‐modified glass slides and nitrocellulose membrane coated slides, were examined and compared. Through this study, we validated the importance of a high protein‐binding capacity of the microarray, and the labeling position of the fluorophore within the aptamer. Purified his‐tagged PFEI (Pseudomonas fluorescence esterase I) was used as a model system. Concentrations of PFEI‐his as low as 30 nM were detectable. These results demonstrate the applicability of aptamers as stable detection molecules in protein assays. Additionally, the reverse phase assay was found to be suitable for the detection of PFEI‐his in cell lysates. This might be of further interest in monitoring of protein production and purification processes.     

The Phaff school of yeast ecology

Herman Jan Phaff's legacy includes pioneering work on the yeast cell envelope and the application of molecular approaches to yeast systematics. Clearly, his interest and knowledge spanned the whole gamut of yeast biology. Yet, his most original and most heartfelt contribution was to our understanding of the position occupied by yeasts in nature. This view developed through the juxtaposition of his childhood exposure to industrial fermentations and his training in the tradition of Beijerinck's Delft School of Microbiology. Through some of Phaff's recent writings, I have attempted to formulate the themes or principles that were implicit to his ecological thinking. Six focal points emerge. (1) Yeasts in themselves are a sufficient object of study. (2) A clear idea of a yeast community cannot be obtained unless the yeast species are correctly identified. (3) Ecologically meaningful conclusions require an adequate sample size. (4) The bacteriological dictum "everything is everywhere" is a poor account of yeast distributions. (5) The habitat is the cornerstone of yeast ecology. (6) Ecology is the most exciting aspect of yeast biology.     

Christiaan Eijkman

One century ago, Christiaan Eijkman was appointed Professor of Bacteriology at the Utrecht University, The Netherlands. Despite his appointment to teach bacteriology, Christiaan Eijkman made his main contribution to medical science not in bacteriology but in nutrition. He discovered that Beri-Beri was not an infection but a nutritient deficiency (later called vitamin-deficiency) and was awarded the Nobel Prize for Medicine in 1929 for these observations. These landmark studies were made in the former Dutch East Indies. Interestingly, the results of his studies were presented in the Dutch language, in the medical journal of the Dutch East Indies. As a professor of Bacteriology, his work was the beginning of an important school in biochemistry in The Netherlands.     

Direction of chromosome rearrangements in Saccharomyces cerevisiae by use of his3 recombinational substrates.

We used the his3 recombinational substrates (his3 fragments) to direct large interchromosomal (translocations) and intrachromosomal (deletions and tandem duplications) rearrangements in the yeast Saccharomyces cerevisiae. In strains completely deleted for the wild-type HIS3 gene, his3 fragments, one containing a deletion of 5' amino acid coding sequences and the other containing a deletion of 3' amino acid coding sequences, were first placed at preselected sites by homologous recombination. His+ revertants that arose via spontaneous mitotic recombination between the two his3 fragments were selected. This strategy was used to direct rearrangements in both RAD52+ and rad52 mutant strains. Translocations occurred in the RAD52+ genetic background and were characterized by orthogonal field alternating gel electrophoresis of yeast chromosomal DNA and by standard genetic techniques. An unexpected translocation was also identified in which HIS3 sequences were amplified. Two types of tandem duplications of the GAL(7, 10, 1) locus were also directed, and one type was not observed in rad52 mutants. Recombination mechanisms are discussed to account for these differences.     

The Problem of Communication in K. S. Stanislavsky's Works

K. S. Stanislavsky (1863-1938) was involved in the study of communication processes long before the development of science prepared the ground for such studies. This was urgently demanded by his self-imposed task of creating an integral, complete, practical system for the actors performance on stage. Neither the science of his time nor existing theatrical experience and theory could provide Stanislavsky with the necessary support for his study of communication.     

Huntington's disease in a Sudanese family from Khartoum

Typical Huntington's disease (HD) was studied in a 40-year-old Sudanese man from Khartoum. He had 51 CAG repeats in the Huntington's gene. It is suspected that his mother and his 16-year-old son (both deceased) were also affected. Up to now, there had only been anecdotal evidence of HD in the Sudanese.