Modulating Hox gene functions during animal body patterning

With their power to shape animal morphology, few genes have captured the imagination of biologists as the evolutionarily conserved members of the Hox clusters have done. Recent research has provided new insight into how Hox proteins cause morphological diversity at the organismal and evolutionary levels. Furthermore, an expanding collection of sequences that are directly regulated by Hox proteins provides information on the specificity of target-gene activation, which might allow the successful prediction of novel Hox-response genes. Finally, the recent discovery of microRNA genes within the Hox gene clusters indicates yet another level of control by Hox genes in development and evolution.     

Molecular mechanisms of platelet exocytosis: requirements for alpha-granule release

Platelets function by secreting components necessary for primary clot formation. This report describes an in vitro assay that measures alpha-granule secretion. Using permeabilized platelets, it is possible to recreate Ca(2+)-stimulated release of platelet factor 4 (PF4) that is ATP- and temperature-dependent. Though other divalent cations can replace Ca(2+) (i.e., Sr(2+), Mn(2+), Zn(2+)), there is no effect of Ba(2+). Analysis by electron microscopy indicates that the in vitro assay also mimics the cytoskeletal rearrangements and granule centralization that occurs upon platelet activation in vivo. Antibody inhibition studies show that PF4 release requires the general membrane fusion protein N-ethylmaleimide-sensitive factor (NSF) and well as the target membrane SNAP receptors (t-SNAREs), syntaxin 2, 4, and SNAP-23. As shown by electron microscopy, the anti-t-SNARE antibodies block granule to target membrane fusion. This finding is unique in that it is the first report of a role for two syntaxins in the same exocytosis event.     

A likelihood‐based approach for assessment of extra‐pair paternity and conspecific brood parasitism in natural populations

Genotypes are frequently used to assess alternative reproductive strategies such as extra‐pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artefacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad‐hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra‐pair paternity and conspecific brood parasitism using a likelihood‐based approach in a new version of program cervus . We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.     

Detecting conspecific brood parasitism using egg morphology in black brant Branta bernicla nigricans

Numerous methods have been proposed to indirectly detect conspecific brood parasitism (CBP) in birds. Egg morphology has been suggested as a predictor of parasitism, assuming that variation in egg size is greater among females than within females. Here we use microsatellite data to assess the use of egg morphology to detect CBP in a sample of black brant Branta bernicla nigricans nests. We attempted to repeat a previously demonstrated technique using cluster analysis and maximum Euclidean distance (MED) to detect parasitized nests within black brant. Additionally we attempted a new technique based on a discriminant function analysis of egg morphology in an attempt to detect brood parasitic eggs. When detecting parasitized nests using egg morphology, the cluster analysis revealed that the MED between the two most dissimilar eggs in each nest was significantly greater for parasitized nests than for non‐parasitized nests (1.62±0.06 and 1.43±0.08, respectively). The extent of overlap in sizes of eggs between parasitized and non‐parasitized nests, however, was such that we were unable to effectively identify parasitized nests. In most cases for each parasitized nest correctly identified, 3 non‐parasitized nests were incorrectly identified as parasitic. When we attempted to detect parasitic eggs we found that parasitic eggs were more different from the expected egg volume than host eggs: mean absolute residual volume of parasitic eggs=2.59±5.79 cm³ while that for host eggs=1.82±2.14 cm³. Overall, we found that the discriminant function analysis was moderately effective in determining whether eggs belonged to the host female using a resubstitution technique (error rate=9.71%) or a jackknife technique (error rate=6.12%). Additionally, we found a higher but moderate error rate when using an independent data set to validate the function (error rate=14.07%). In both cases, however, parasitic eggs accounted for most of the error and were not correctly classified 75%, 70% and 100% of the time respectively. We suggest when developing a predictive function for detecting conspecific brood parasitism based on egg morphology that an appropriate technique be used to validate the function, particularly those techniques that utilize unambiguous identifiers such as molecular and protein fingerprinting techniques.     

Modifications of the C6-substituent of penicillin sulfones with the goal of improving inhibitor recognition and efficacy

In order to evaluate the importance of a hydrogen-bond donating substituent in the design of β-lactamase inhibitors, a series of C6-substituted penicillin sulfones, lacking a C2′ substituent, and having an sp³ hybridized C6, was prepared and evaluated against a representative classes A and C β-lactamases. It was found that a C6 hydrogen-bond donor is necessary for good inhibitory activity, but that this feature alone is not sufficient in this series of C6β-substituted penicillin sulfones. Other factors which may impact the potency of the inhibitor include the steric bulk of the C6 substituent (e.g., methicillin sulfone) which may hinder recognition in the class A β-lactamases, and also high similarity to the natural substrates (e.g., penicillin G sulfone) which may render the prospective inhibitor a good substrate of both classes of enzyme. The best inhibitors had non-directional hydrogen-bonding substituents, such as hydroxymethyl, which may allow sufficient conformational flexibility of the acyl-enzyme for abstraction of the C6 proton by E166 (class A), thus promoting isomerization to the β-aminoacrylate as a stabilized acyl-enzyme.     

Anisotropic Material Properties of Wild-Type and Tectb−/− Tectorial Membranes

The tectorial membrane (TM) is an extracellular matrix that is directly coupled with the mechanoelectrical receptors responsible for sensory transduction and amplification. As such, the TM is often hypothesized to play a key role in the remarkable sensory abilities of the mammalian cochlea. Genetic studies targeting TM proteins have shown that changes in TM structure dramatically affect cochlear function in mice. Precise information about the mechanical properties of the TMs of wild-type and mutant mice at audio frequencies is required to elucidate the role of the TM and to understand how these genetic mutations affect cochlear mechanics. In this study, images of isolated TM segments are used to determine both the radial and longitudinal motions of the TM in response to a harmonic radial excitation. The resulting longitudinally propagating radial displacement and highly spatially dependent longitudinal displacement are modeled using finite-element models that take into account the anisotropy and finite dimensions of TMs. An automated, least-square fitting algorithm is used to find the anisotropic material properties of wild-type and Tectb^?/? mice at audio frequencies. Within the auditory frequency range, it is found that the TM is a highly viscoelastic and anisotropic structure with significantly higher stiffness in the direction of the collagen fibers. Although no decrease in the stiffness in the fiber direction is observed, the stiffness of the TM in shear and in the transverse direction is found to be significantly reduced in Tectb^?/? mice. As a result, TMs of the mutant mice tend to be significantly more anisotropic within the frequency range examined in this study. The effects of the Tectb^?/? mutation on the TM’s anisotropic material properties may be responsible for the changes in cochlear tuning and sensitivity that have been previously reported for these mice.     

CTNS mutations in an American-based population of cystinosis patients.

Nephropathic cystinosis is an autosomal recessive lysosomal storage disease characterized by renal failure at 10 years of age and other systemic complications. The gene for cystinosis, CTNS, has 12 exons. Its 2.6-kb mRNA codes for a 367-amino-acid putative cystine transporter with seven transmembrane domains. Previously reported mutations include a 65-kb "European" deletion involving marker D17S829 and 11 small mutations. Mutation analysis of 108 American-based nephropathic cystinosis patients revealed that 48 patients (44%) were homozygous for the 65-kb deletion, 2 had a smaller major deletion, 11 were homozygous and 3 were heterozygous for 753G-->A (W138X), and 24 had 21 other mutations. In 20 patients (19%), no mutations were found. Of 82 alleles bearing the 65-kb deletion, 38 derived from Germany, 28 from the British Isles, and 4 from Iceland. Eighteen new mutations were identified, including the first reported missense mutations, two in-frame deletions, and mutations in patients of African American, Mexican, and Indian ancestry. CTNS mutations are spread throughout the leader sequence, transmembrane, and nontransmembrane regions. According to a cystinosis clinical severity score, homozygotes for the 65-kb deletion and for W138X have average disease, whereas mutations involving the first amino acids prior to transmembrane domains are associated with mild disease. By northern blot analysis, CTNS was not expressed in patients homozygous for the 65-kb deletion but was expressed in all 15 other patients tested. These data demonstrate the origins of CTNS mutations in America and provide a basis for possible molecular diagnosis in this population.