Generalized crystallography

X-ray crystal structure analysis can now be seen as a special kind of microscopy which is being extended to the recognition and examination of many kinds of ordered structure more general than crystals and which leads to their synthesis or construction by various methods. Electron microscopy and many other techniques now combine to give a coherent science of structure at the scale range of Ångstroms to microns, atoms to assemblies visible to the eye, which should continue to be called crystallography although it overlaps with nanotechnology, molecular biology, and solid state physics. Most generally, a crystal is a structure the description of which is much smaller than the structure itself and this view leads to the consideration of structures as carriers of information and on to wider concerns with growth, form, morphogenesis, and life itself

Lucretius or the philosophy of chemistry

A world view deriving from the objective knowledge acquired by the physical sciences is contrasted with the fashionable subjective philosophical view that all systems of thought are equally valid ways of structuring the universe. As Lucretius guessed, atoms are real and are not simply arbitrary constructs to explain the observations. Mathematics and computing have an important role in permitting long and sophisticated arguments to be carried through

The shape of two-dimensional space

Genomics, so fashionable today, is only half of the secret of life. The other half of the secret is shape, form, morphogenesis and metamorphosis. The gene may prescribe what is synthesised, but the proteins appear and operate in a pre-existing environment which they then change. The first step towards life is the appearance of a micelle, a spherical membrane, a surface which separates the world into inside and outside. We are here concerned with surfaces, with a particular subset of two-dimensional manifolds embedded in three-dimensional Euclidean space, namely the non-self-intersecting, periodic minimal surfaces of cubic symmetry, which separate the world into two regions as an infinite plane would do, but with much more complex topologies. Like the Platonic solids , these cubic surfaces are geometrical absolutes and have distinctive topologies but entail no arbitrary parameters . The objective is to enumerate at least some of these surfaces, for probably an infinite number answer to this description, to draw attention to their geometry and to point to some of their applications and occurrences on various scales between mega-engineering and nano-technology. These objects are solutions looking for problems

From “the dialectics of nature” to the inorganic gene

The concept of projection from one space to another, with a consequent loss of information, can be seen in the relationships of gene to protein and language description to real situation. Such a transformation can only be reversed if extra external information is re-supplied. The genetic algorithm embodying this idea is now used in applied mathematics for exploring a configuration space. Such a dialectic – transformation back and forth between two kinds of description – extends the traditional Hegelian concept used by Engels and others of change as resulting from a resolution of the conflict of two opposing tendencies and provides for evolution of the joint system

Periodic minimal surfaces of cubic symmetry

A survey of cubic minimal surfaces is presented, based on the concept of fundamental surface patches and their relation to the asymmetric units of the space groups. The software Surface Evolver has been used to test for stability and to produce graphic displays. Particular emphasis is given to those surfaces that can be generated by a finite piece bounded by straight lines. Some new varieties have been found and a systematic nomenclature is introduced, which provides a symbol (a ‘gene’) for each triply-periodic minimal surface that specifies the surface unambiguously

Serratia marcescens, the “Flame” Strain: The Genesis of a New Variant A Newly Described Strain with Prolific Pigment Produced at High Temperature

Serratia marcescens, a Gram-negative, rod-shaped, facultative anaerobe (Fig. 1), is ubiquitous in water, soil, and natural settings. It is easily grown in the lab and may serve as an ideal model for adaptation studies because of the natural color variation of S. marcescens (Gillen 2008). In this paper, we describe a new variant with prolific pigment (prodigiosin) production at high temperatures. In the wild and in buildings, S. marcescens is noted for the production of a bright red pigment called prodigiosin (Williams 1973). We have found a new strain that appears to have adapted to a relatively new pond system called Liberty Library Lake. It produces pigment up to 40°C without any enrichment to media. Most wild-type strains, like NIMA, produce pigment normally up to 30°C, but with extensive enrichment, wild-type strains can produce pigment up to 40°C. This new strain, called the “Flame” strain, not only produces prodigiosin to 39–40°C but also in higher abundance at 35°C and at a brighter hue. NIMA strains can produce pigment at 39–40°C with Serratia Synergy Agar (glycerol, peptone, agar) but not on TSA nor any common agar. It takes significant enhancement for any other Serratia marcescens strains to produce pigment even at 35°C. The Flame strain’s brief appearance in a local, small lake appears to be a phenotypic diversification and adaptation to an environmental perturbation this past school year. The environmental stress prior to its appearance was an autumn drought. Eventually, heavy rainfall occurred and the new strain was discovered. Its appearance coincided with an unusually high abundance of coliforms, avian Giardia, and Cryptosporidium, along with chemical treatment of the lake. The unusual conditions seem to favor a rapid phenotypic diversification and adaptation. The new strain still retains the pigment production at nearly 10°C higher for “normal” prodigiosin production by wild-type Serratia marcescens. This genesis of this new strain seems to have occurred as special conditions favored this new variant. It may be closer to a “proto-type” (ancestral) strain than to more common wild-type strains, like NIMA and BS303. It appears that most wild-type strains, like NIMA and BS303, may have lost this information over time since added enrichment is necessary to produce pigment at 39–40°C. The unusual conditions may have selected for this newly adapted strain to be common for a short time. Also as conditions returned to “normal,” a common wild-type strain reappeared at the local lake, and the Flame strain was no longer found. The objective of this article is to explain the mysterious origin of a new strain of Serratia marcescens that produces prodigiosin up to 40°C without any enrichment to media. This strain can naturally produce prolific pigment that is a bright, flame-red. Since Serratia marcescens offers protection from other microbes, UV light, and drought, it is a wonderful example of intelligent design commonly seen in the microbial world

Lucretius: atoms and opinions

It is argued that the scientific programme most clearly articulated by Lucretius is still appropriate today, although it continues to represent a minority view of the world. In 'De rerum natura' Lucretius formulated the goals of explaining, without religious or supernatural assumptions, the properties of all living and non-living things in terms of the emergent properties of atoms. We examine five topics: atoms - structure underlies function; group theory and the breakdown of exact equivalence; the emergence of complex properties from simple units; the parallel between letters (of the alphabet) and atoms in the building of complex structures; and the coming coalescence of the mental and physical worlds

East African lake evidence for Pliocene millennial-scale climate variability

Late Cenozoic climate history in Africa was punctuated by episodes of variability, characterized by the appearance and disappearance of large freshwater lakes within the East African Rift Valley. In the Baringo-Bogoria basin, a well-dated sequence of diatomites and fluviolacustrine sediments documents the precessionally forced cycling of an extensive lake system between 2.70 Ma and 2.55 Ma. One diatomite unit was studied, using the oxygen isotope composition of diatom silica combined with X-ray fluorescence spectrometry and taxonomic assemblage changes, to explore the nature of climate variability during this interval. Data reveal a rapid onset and gradual decline of deepwater lake conditions, which exhibit millennial-scale cyclicity of ∼1400–1700 yr, similar to late Quaternary Dansgaard-Oeschger events. These cycles are thought to reflect enhanced precipitation coincident with increased monsoonal strength, suggesting the existence of a teleconnection between the high latitudes and East Africa during this period. Such climatic variability could have affected faunal and floral evolution at the time

Regulator of G-protein signalling 2 mRNA is differentially expressed in mammary epithelial subpopulations and over-expressed in the majority of breast cancers

To understand which signalling pathways become deregulated in breast cancer, it is necessary to identify functionally significant gene expression patterns in the stem, progenitor, transit amplifying and differentiated cells of the mammary epithelium. We have previously used the markers 33A10, CD24 and Sca-1 to identify mouse mammary epithelial cell subpopulations. We now investigate the relationship between cells expressing these markers and use gene expression microarray analysis to identify genes differentially expressed in the cell populations. METHODS: Freshly isolated primary mouse mammary epithelial cells were separated on the basis of staining with the 33A10 antibody and an alpha-Sca-1 antibody. The populations identified were profiled using gene expression microarray analysis. Gene expression patterns were confirmed on normal mouse and human mammary epithelial subpopulations and were examined in a panel of breast cancer samples and cell lines. RESULTS: Analysis of the separated populations demonstrated that Sca-1- 33A10High stained cells were estrogen receptor alpha (Esr1)- luminal epithelial cells, whereas Sca-1+ 33A10Low/- stained cells were a mix of nonepithelial cells and Esr1+ epithelial cells. Analysis of the gene expression data identified the gene Rgs2 (regulator of G-protein signalling 2) as being highly expressed in the Sca-1- 33A10Low/- population, which included myoepithelial/basal cells. RGS2 has previously been described as a regulator of angiotensin II receptor signalling. Gene expression analysis by quantitative real-time RT-PCR of cells separated on the basis of CD24 and Sca-1 expression confirmed that Rgs2 was more highly expressed in mouse myoepithelial/basal mammary cells than luminal cells. This expression pattern was conserved in normal human breast cells. Functional analysis demonstrated RGS2 to be a modulator of oxytocin receptor signalling. The potential significance of RGS2 expression in breast cancer was demonstrated by semi-quantitative RT-PCR analysis, data mining and quantitative real-time RT-PCR approaches, which showed that RGS2 was expressed in the majority of solid breast cancers at much higher levels than in normal human mammary cells. CONCLUSION: Molecular analysis of prospectively isolated mammary epithelial cells identified RGS2 as a modulator of oxytocin receptor signalling, which is highly expressed in the myoepithelial cells. The RGS2 gene, but not the oxytocin receptor, was also shown to be over-expressed in the majority of breast cancers, identifying the product of this gene, or the pathway(s) it regulates, as potentially significant therapeutic targets