Aquaporin-1, nothing but a water channel

Aquaporin-1 (AQP1) is a membrane channel that allows rapid water movement driven by a transmembrane osmotic gradient. It was claimed to have a secondary function as a cyclic nucleotide-gated ion channel. However, upon reconstitution into planar bilayers, the ion channel exhibited a 10-fold lower single channel conductance than in Xenopus oocytes and a 100-fold lower open probability (<10(-6)) of doubtful physiological significance (Saparov, S. M., Kozono, D., Rothe, U., Agre, P., and Pohl, P. (2001) J. Biol. Chem. 276, 31515-31520). Investigating AQP1 expressed in human embryonic kidney cells, we now have shown that the discrepancy is not due to alterations of AQP1 properties upon reconstitution into bilayers but rather to regulatory processes of the oocyte expression system that may have been misinterpreted as AQP1 ion channel activity. As confirmed by laser scanning reflection microscopy, from 0.8 to 1.4 x 10(6) AQP1 copies/cell contributed to osmotic cell swelling. The proper plasma membrane localization was confirmed by observing the fluorescence of the N-terminal yellow fluorescent protein tag. Whole-cell patch clamp experiments of wild type or tagged AQP1-expressing cells revealed that neither cGMP nor cAMP mediated ion channel activity. The lack of significant CNG ion channel activity rules out a secondary role of AQP1 water channels in cellular signal transduction.     

Escherichia coli gets a new virus but it's nothing to sneeze at

For the past two decades virologists have strived to make full-length clones of viral genomes that, on transfection into permissive eukaryotic cells, initiate a productive infection. The large variety of viral RNA and DNA genome structures, as well as different replication strategies, has required investigators to develop new approaches to produce infectious DNA in Escherichia coli. A member of the poxviridae, one of the most complex virus families, has now been made into an infectious clone in E. coli for the first time. Although the isolation was complicated, the infectious clone will greatly simplify future genetic studies of the virus.     

The whole alignment and nothing but the alignment: the problem of spurious alignment flanks

Pairwise sequence alignment is a ubiquitous tool for inferring the evolution and function of DNA, RNA and protein sequences. It is therefore essential to identify alignments arising by chance alone, i.e. spurious alignments. On one hand, if an entire alignment is spurious, statistical techniques for identifying and eliminating it are well known. On the other hand, if only a part of the alignment is spurious, elimination is much more problematic. In practice, even the sizes and frequencies of spurious subalignments remain unknown. This article shows that some common scoring schemes tend to overextend alignments and generate spurious alignment flanks up to hundreds of base pairs/amino acids in length. In the UCSC genome database, e.g. spurious flanks probably comprise >18% of the human–fugu genome alignment. To evaluate the possibility that chance alone generated a particular flank on a particular pairwise alignment, we provide a simple ‘overalignment’ P-value. The overalignment P-value can identify spurious alignment flanks, thereby eliminating potentially misleading inferences about evolution and function. Moreover, by explicitly demonstrating the tradeoff between over- and under-alignment, our methods guide the rational choice of scoring schemes for various alignment tasks.     

Automating digital leaf measurement: the tooth, the whole tooth, and nothing but the tooth

Many species of plants produce leaves with distinct teeth around their margins. The presence and nature of these teeth can often help botanists to identify species. Moreover, it has long been known that more species native to colder regions have teeth than species native to warmer regions. It has therefore been suggested that fossilized remains of leaves can be used as a proxy for ancient climate reconstruction. Similar studies on living plants can help our understanding of the relationships. The required analysis of leaves typically involves considerable manual effort, which in practice limits the number of leaves that are analyzed, potentially reducing the power of the results. In this work, we describe a novel algorithm to automate the marginal tooth analysis of leaves found in digital images. We demonstrate our methods on a large set of images of whole herbarium specimens collected from Tilia trees (also known as lime, linden or basswood). We chose the genus Tilia as its constituent species have toothed leaves of varied size and shape. In a previous study we extracted [Formula: see text] leaves automatically from a set of [Formula: see text] images. Our new algorithm locates teeth on the margins of such leaves and extracts features such as each tooth's area, perimeter and internal angles, as well as counting them. We evaluate an implementation of our algorithm's performance against a manually analyzed subset of the images. We found that the algorithm achieves an accuracy of 85% for counting teeth and 75% for estimating tooth area. We also demonstrate that the automatically extracted features are sufficient to identify different species of Tilia using a simple linear discriminant analysis, and that the features relating to teeth are the most useful.     

Hydrogen-bonded turns in proteins: the case for a recount

Beta-turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble beta-turns but lack the characteristic N-H(i) --> O=C(i - 3) hydrogen bond of an authentic beta-turn. Here, we identify potential hydrogen-bonded beta-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither alpha-helix nor beta-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded beta-turns. In particular, 33% of coil library residues were classified as beta-turns prior to minimization. After minimization, 45% of such residues could be classified as beta-turns, with another 8% in 3(10) helixes (which closely resemble type III beta-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure.     

Cdc14B: When a good kid turns bad

Comment on: Chiesa M, et al. Cell Cycle 2011; 10:1607-17.     

Acrosomal actin: twists and turns of a versatile filament

A new electron cryomicroscopic reconstruction of an actin-scruin bundle from Limulus sperm reveals details about the enormous structural plasticity within F-actin. The twist and tilt of the actin subunits show very large deviations from ideal F-actin, providing clues about actin dynamics.     

Lycramine brilliant blue JL: a new stain for human megakaryocytes

Using the acrylic textile dye Lycramine brilliant blue JL, mature and immature megakaryocytes from human bone marrow specimens stained metachromatically bright lavender. This coloration was not observed in other types of bone marrow cells. After digestion with either diastase or ribonuclease, subsequent staining of marrow specimens did not reveal a significant diminution of the intensity of staining of megakaryocytes. However, after incubation with hyaluronidase followed by staining with Lycramine brilliant blue JL, staining of megakaryocyte cytoplasm was either imperceptible or very pale blue. Accordingly, at least one of the substances responsible for the staining reaction is acid mucopolysaccharide in the cytoplasm of megakaryocytes. With further experience and comparison with established immunologic and cytochemical techniques, staining of megakaryocytes with Lycramine brilliant blue JL may be a useful addition to the cytochemistry of blood and bone marrow cells.     

Xenotransplantation: a problematic world behind a glamorous facade

The discussion about the ethics of xenotransplantation seems to focus upon the benefits for individual patients and the potential risks for human society, in general, to contract a newly emerging retrovirus. In these risk-benefit considerations, the moral concern for the research animals involved appears to be absent. This is remarkable, because the presumed successful xenograft is not expected very soon. A lot of basic problems in pig and primate xenotransplantations still need solving. These new experiments in our own biomedical laboratories raise questions regarding animal welfare and ethical justification in the light of possible alternative strategies. In this article, I discuss some of the moral issues related to preclinical, fundamental xenotransplantation research.     

Microscopic, biochemical, and molecular characteristics of the Chilean Blob and a comparison with the remains of other sea monsters: nothing but whales

We have employed electron microscopic, biochemical, and molecular techniques to clarify the species of origin of the "Chilean Blob," the remains of a large sea creature that beached on the Chilean coast in July 2003. Electron microscopy revealed that the remains are largely composed of an acellular, fibrous network reminiscent of the collagen fiber network in whale blubber. Amino acid analyses of an acid hydrolysate indicated that the fibers are composed of 31% glycine residues and also contain hydroxyproline and hydroxylysine, all diagnostic of collagen. Using primers designed to the mitochondrial gene nad2, an 800-bp product of the polymerase chain reaction (PCR) was amplified from DNA that had been purified from the carcass. The DNA sequence of the PCR product was 100% identical to nad2 of sperm whale (Physeter catadon). These results unequivocally demonstrate that the Chilean Blob is the almost completely decomposed remains of the blubber layer of a sperm whale. This identification is the same as those we have obtained before from other relics such as the so-called giant octopus of St. Augustine (Florida), the Tasmanian West Coast Monster, two Bermuda Blobs, and the Nantucket Blob. It is clear now that all of these blobs of popular and cryptozoological interest are, in fact, the decomposed remains of large cetaceans.