The CATH extended protein-family database: providing structural annotations for genome sequences.

An automatic sequence search and analysis protocol (DomainFinder) based on PSI-BLAST and IMPALA, and using conservative thresholds, has been developed for reliably integrating gene sequences from GenBank into their respective structural families within the CATH domain database (http://www.biochem.ucl.ac.uk/bsm/cath_new). DomainFinder assigns a new gene sequence to a CATH homologous superfamily provided that PSI-BLAST identifies a clear relationship to at least one other Protein Data Bank sequence within that superfamily. This has resulted in an expansion of the CATH protein family database (CATH-PFDB v1.6) from 19,563 domain structures to 176,597 domain sequences. A further 50,000 putative homologous relationships can be identified using less stringent cut-offs and these relationships are maintained within neighbour tables in the CATH Oracle database, pending further evidence of their suggested evolutionary relationship. Analysis of the CATH-PFDB has shown that only 15% of the sequence families are close enough to a known structure for reliable homology modeling. IMPALA/PSI-BLAST profiles have been generated for each of the sequence families in the expanded CATH-PFDB and a web server has been provided so that new sequences may be scanned against the profile library and be assigned to a structure and homologous superfamily.     

Acquired ptosis: a reexamination of etiology and treatment

The etiology of acquired ptosis is almost always disinsertion of the levator aponeurosis from the tarsal plate. As opposed to congenital ptosis, where levator resection is required to compensate for muscle weakness, acquired ptosis can be consistently treated with simple levator reattachment. This study examines both the diagnostic and anatomic etiology of acquired ptosis in 80 consecutive patients. Although dermatochalasis, trauma with orbital hematoma, orbital swelling, anophthalmos, and multiple other diverse clinical etiologies were responsible for this condition, the anatomic etiology was identical in 79 of the patients--levator disinsertion. Cadaver studies demonstrate that the levator aponeurosis inserts into the tarsal plate through multiple flimsy, fibrous attachments. Any condition that results in either excess weight to the eyelids or excess muscular pull can disrupt these fibers. A modification of the external approach is described that allows rapid identification of the levator aponeurosis and permits accurate repair. Complete repair was achieved in the majority of the cases, and there were no instances of overcorrection.     

Water permeability of plant cuticular membranes: the effects of humidity and temperature on the permeability of non-isolated cuticles of onion bulb scales

Abstract. Water permeability of cuticular membranes (CM) from the inner bulb scales of Allium cepa has been investigated. CM have a thickness ranging from 0.6 to 1.3 μm. They are composed of a thin (120–200 nm) lamellated cuticle proper and a thicker (300–900 nm) cuticular layer. Permeability coefficients for diffusion of water across these thin membranes are very low (4 × lO⁻¹⁰ms⁻¹⁰). There was no difference in permeability of CM from successive scales of the same onion. Extraction of soluble cuticular lipids (SCL) with chloroform increased permeability by a factor of 1350 to 2050. Preliminary data indicate that only 1 μg cm⁻¹⁰ of SCL are removed by this treatment, hydrocarbons being the main (75%) consistuent. Permeability coefficients of cuticular transpiration were little affected by relative humidity, showing that transport is limited by a hydrophobic barrier that lacks dipoles. However, following extraction, permeability of the membranes depended strongly on humidity due to the presence of polar functional groups in the polymer matrix. Soluble cuticular lipids undergo a phase transition around 47°C. Temperatures higher than that irreversibly increased water permeability.     

The deciduous dentition and dental replacement in the Eocene bat Palaeochiropteryx tupaiodon from Messel: The primitive condition and beginning of specialization of milk teeth among Chiroptera

The deciduous dentition and tooth replacement pattern of Palaeochiropteryx tupaiodon from the early Middle Eocene of Messel, near Frankfurt, Germany, are described. Ontogenetic states include fetuses to subadults. The posterior portion of the deciduous dentition (dP3-4) still shows the primitive eutherian condition of molarization, while the anterior part (dI-dC) was already engaged in the evolution of the highly derived condition found in living bats for clinging to the mother's fur. A styliform and sharp anterior dentition is considered a prerequisite in earliest chiropteran evolution. The greatly modified milk teeth of all living bats developed in different clades by parallel evolution under high selective pressure. The tiny and, at initial stages, poorly calcified teeth are substantiated by a newly developed microradiographic technique which is described in detail.     

An Inverse Analysis Approach to the Characterization of Chemical Transport in Paints

The ability to directly characterize chemical transport and interactions that occur within a material (i.e., subsurface dynamics) is a vital component in understanding contaminant mass transport and the ability to decontaminate materials. If a material is contaminated, over time, the transport of highly toxic chemicals (such as chemical warfare agent species) out of the material can result in vapor exposure or transfer to the skin, which can result in percutaneous exposure to personnel who interact with the material. Due to the high toxicity of chemical warfare agents, the release of trace chemical quantities is of significant concern. Mapping subsurface concentration distribution and transport characteristics of absorbed agents enables exposure hazards to be assessed in untested conditions. Furthermore, these tools can be used to characterize subsurface reaction dynamics to ultimately design improved decontaminants or decontamination procedures. To achieve this goal, an inverse analysis mass transport modeling approach was developed that utilizes time-resolved mass spectroscopy measurements of vapor emission from contaminated paint coatings as the input parameter for calculation of subsurface concentration profiles. Details are provided on sample preparation, including contaminant and material handling, the application of mass spectrometry for the measurement of emitted contaminant vapor, and the implementation of inverse analysis using a physics-based diffusion model to determine transport properties of live chemical warfare agents including distilled mustard (HD) and the nerve agent VX.