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

Exome sequencing identifies a missense variant in EFEMP1 co-segregating in a family with autosomal dominant primary open-angle glaucoma

Primary open-angle glaucoma (POAG) is a clinically important and genetically heterogeneous cause of progressive vision loss as a result of retinal ganglion cell death. Here we have utilized trio-based, whole-exome sequencing to identify the genetic defect underlying an autosomal dominant form of adult-onset POAG segregating in an African-American family. Exome sequencing identified a novel missense variant (c.418C>T, p.Arg140Trp) in exon-5 of the gene coding for epidermal growth factor (EGF) containing fibulin-like extracellular matrix protein 1 (EFEMP1) that co-segregated with disease in the family. Linkage and haplotype analyses with microsatellite markers indicated that the disease interval overlapped a known POAG locus (GLC1H) on chromosome 2p. The p.Arg140Trp substitution was predicted in silico to have damaging effects on protein function and transient expression studies in cultured cells revealed that the Trp140-mutant protein exhibited increased intracellular accumulation compared with wild-type EFEMP1. In situ hybridization of the mouse eye with oligonucleotide probes detected the highest levels of EFEMP1 transcripts in the ciliary body, cornea, inner nuclear layer of the retina, and the optic nerve head. The recent finding that a common variant near EFEMP1 was associated with optic nerve-head morphology supports the possibility that the EFEMP1 variant identified in this POAG family may be pathogenic

Ultrasound-Guided Suture Tape Augmentation and Stabilization of the Medial Collateral Ligament

Management of medial collateral ligament (MCL) injuries usually consists of time and conservative management; however, patients are typically immobilized and need extensive time to return to sport. Although the MCL has been shown to have the ability to heal given time, surgical management is still sometimes needed to provide stability to the knee. Operative techniques vary in methodology, but are typically highly invasive and technically demanding. In the event of multiligamentous or severe injuries, reinforcing the MCL with an ultrahigh-strength, 2-mm-wide suture tape allows for early functional rehabilitation, permitting the native MCL tissue to heal and avoiding late reconstructions. This technical report details an ultrasound-guided technique for the percutaneous suture tape augmentation and stabilization of the MCL with or without repair. Ultrasound allows for anatomic percutaneous placement of the sockets, as opposed to landmark palpation guidance that has proven to be unreliable. This is a simple, quick procedure that provides instant stability to the MCL with or without operating on the ligament itself, allowing patients to return to activity faster with the reduced risk of reinjury due to less muscle atrophy and loss of function

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