Catalytic site-selective synthesis and evaluation of a series of erythromycin analogs

The generation of a series of analogs of erythromycin A (EryA, 2) is described. In this study, we compared two peptide-based catalysts-one originally identified from a catalyst screen (5) and its enantiomer (ent-5)-for the selective functionalization of EryA. The semi-synthetic analogs were subjected to MIC evaluation with two bacterial strains and compared to unfunctionalized EryA.     

Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism

Bacterial NadM-Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide (NMN) adenylyltransferase and an ADP-ribose (ADPR) pyrophosphatase domain. While most members of this enzyme family, such as that from a model cyanobacterium Synechocystis sp., are involved primarily in nicotinamide adenine dinucleotide (NAD) salvage/recycling pathways, its close homolog in a category-A biodefense pathogen, Francisella tularensis, likely plays a central role in a recently discovered novel pathway of NAD de novo synthesis. The crystal structures of NadM-Nudix from both species, including their complexes with various ligands and catalytic metal ions, revealed detailed configurations of the substrate binding and catalytic sites in both domains. The structure of the N-terminal NadM domain may be exploited for designing new antitularemia therapeutics. The ADPR binding site in the C-terminal Nudix domain is substantially different from that of Escherichia coli ADPR pyrophosphatase, and is more similar to human NUDT9. The latter observation provided new insights into the ligand binding mode of ADPR-gated Ca2+ channel TRPM2.     

The “Beauty Myth” Is No Myth

The phenomenon of apparently greater emphasis on human female physical attractiveness has spawned an array of explanatory responses, but the great majority can be broadly categorized as either evolutionary or social constructivist in nature. Both perspectives generate distinct and testable predictions. If, as Naomi Wolf (The beauty myth: How images of female beauty are used against women. New York: William Morrow, [originally published in 1991], 2002) and others have argued, greater emphasis on female attractiveness is part of a predominantly Western “beauty myth,” then an analysis of a culturally diverse sample should reveal marked fluctuation in gendered attractiveness emphasis: there should be significant numbers of cultures in which male and female attractiveness are equally emphasized, and cultures in which male attractiveness receives more emphasis. On the other hand, an evolutionary perspective suggests that disproportionate emphasis on female attractiveness will be a universal or near-universal phenomenon. To test these hypotheses, we tallied references to male versus female attractiveness in 90 collections of traditional folktales from 13 diverse cultural areas. The results are consistent with the evolutionary predictions and inconsistent with the constructivist predictions. Across culture areas information on physical attractiveness was much more likely to be conveyed for female characters. Together with other recent studies, these results suggest that the main elements of the beauty myth are not myths: there are large areas of overlap in the attractiveness judgments of diverse populations, and cross-cultural emphasis on physical attractiveness appears to fall principally upon women.     

Phylogeny, evolutionary history, and biogeography of Oriental-Australian rear-fanged water snakes (Colubroidea: Homalopsidae) inferred from mitochondrial and nuclear DNA sequences

Homalopsid snakes are widely distributed throughout Southeast Asia and form the ecologically dominant component of the herpetofauna over much of their range. Although they are considered well differentiated from other colubrid lineages, several aspects of their radiation including within-family relationships, temporal patterns of species diversification, and biogeographic history remain under studied. We analyzed sequence data from four genes (three mitochondrial and one nuclear) for 22 species of the Homalopsidae to generate the most comprehensive phylogeny of the family to date. We also estimated divergence times within the family using a model of independent but log-normally distributed rates of evolution in conjunction with two external fossil calibrations. Using this chronogram, we inferred historical patterns of species diversification within the family. Finally, we used previously published sequence data for 172 snake species to test for the monophyly of the Homalopsidae. Phylogenetic analysis reveals strong support for homalopsid monophyly with an estimate age of the crown group of approximately 22 MYA. The family comprises three major clades which all originated 18-20 MY. Lineage through time plots reveal that homalopsids experienced a significantly higher rate of effective cladogenesis in their early history, consistent with a hypothesis of adaptive radiation. We discuss several Miocene and Pliocene paleogeographic factors that might underlie observed patterns of temporal diversification and biogeography.     

Influence of pelvis position on the activation of abdominal and hip flexor muscles

A pelvic position has been sought that optimizes abdominal muscle activation while diminishing hip flexor activation. Thus, the objective of the study was to investigate the effect of pelvic position and the Janda sit-up on trunk muscle activation. Sixteen male volunteers underwent electromyographic (EMG) testing of their abdominal and hip flexor muscles during a supine isometric double straight leg lift (DSLL) with the feet held approximately 5 cm above a board. The second exercise (Janda sit-up) was a sit-up action where participants simultaneously contracted the hamstrings and the abdominal musculature while holding an approximately 45 degrees angle at the knee. Root mean square surface electromyography was calculated for the Janda sit-up and DSLL under 3 pelvic positions: anterior, neutral, and posterior pelvic tilt. The selected muscles were the upper and lower rectus abdominis (URA, LRA), external obliques, lower abdominal stabilizers (LAS), rectus femoris, and biceps femoris. The Janda sit-up position demonstrated the highest URA and LRA activation and the lowest rectus femoris activation. The Janda sit-up and the posterior tilt were significantly greater (p < 0.01 and p < 0.05, respectively) than the anterior tilt for the URA and LRA muscles. Activation levels of the URA and LRA in neutral pelvis were significantly (p < 0.01 and p < 0.05, respectively) less than the Janda sit-up position, but not significantly different from the posterior tilt. No significant differences in EMG activity were found for the external obliques or LAS. No rectus femoris differences were found in the 3 pelvis positions. The results of this study indicate that pelvic position had a significant effect on the activation of selected trunk and hip muscles during isometric exercise, and the activation of the biceps femoris during the Janda sit-up reduced the activation of the rectus femoris while producing high levels of activation of the URA and LRA.     

Human immunodeficiency virus type 1 Vpr-binding protein VprBP, a WD40 protein associated with the DDB1-CUL4 E3 ubiquitin ligase, is essential for DNA replication and embryonic development

Damaged DNA binding protein 1, DDB1, bridges an estimated 90 or more WD40 repeats (DDB1-binding WD40, or DWD proteins) to the CUL4-ROC1 catalytic core to constitute a potentially large number of E3 ligase complexes. Among these DWD proteins is the human immunodeficiency virus type 1 (HIV-1) Vpr-binding protein VprBP, whose cellular function has yet to be characterized but has recently been found to mediate Vpr-induced G₂ cell cycle arrest. We demonstrate here that VprBP binds stoichiometrically with DDB1 through its WD40 domain and through DDB1 to CUL4A, subunits of the COP9/signalsome, and DDA1. The steady-state level of VprBP remains constant during interphase and decreases during mitosis. VprBP binds to chromatin in a DDB1-independent and cell cycle-dependent manner, increasing from early S through G₂ before decreasing to undetectable levels in mitotic and G₁ cells. Silencing VprBP reduced the rate of DNA replication, blocked cells from progressing through the S phase, and inhibited proliferation. VprBP ablation in mice results in early embryonic lethality. Conditional deletion of the VprBP gene in mouse embryonic fibroblasts results in severely defective progression through S phase and subsequent apoptosis. Our studies identify a previously unknown function of VprBP in S-phase progression and suggest the possibility that HIV-1 Vpr may divert an ongoing chromosomal replication activity to facilitate viral replication.     

EPO-KB: a searchable knowledge base of biomarker to protein links

The knowledge base EPO-KB (Empirical Proteomic Ontology Knowledge Base) is based on an OWL ontology that represents current knowledge linking mass-to-charge (m/z) ratios to proteins on multiple platforms including Matrix Assisted Laser/Desorption Ionization (MALDI) and Surface Enhanced Laser/Desorption Ionization (SELDI)--Time of Flight (TOF). At present, it contains information on m/z ratio to protein links that were extracted from 120 published research papers. It has a web interface that allows researchers to query and retrieve putative proteins that correspond to a user-specified m/z ratio. EPO-KB also allows automated entry of additional m/z ratio to protein links and is expandable to the addition of gene to protein and protein to disease links. AVAILABILITY: http://www.dbmi.pitt.edu/EPO-KB     

Fibroblast growth factor receptor signaling is essential for lens fiber cell differentiation

The vertebrate lens provides an excellent model to study the mechanisms that regulate terminal differentiation. Although fibroblast growth factors (FGFs) are thought to be important for lens cell differentiation, it is unclear which FGF receptors mediate these processes during different stages of lens development. Deletion of three FGF receptors (Fgfr1-3) early in lens development demonstrated that expression of only a single allele of Fgfr2 or Fgfr3 was sufficient for grossly normal lens development, while mice possessing only a single Fgfr1 allele developed cataracts and microphthalmia. Profound defects were observed in lenses lacking all three Fgfrs. These included lack of fiber cell elongation, abnormal proliferation in prospective lens fiber cells, reduced expression of the cell cycle inhibitors p27^kip1 and p57^kip2, increased apoptosis and aberrant or reduced expression of Prox1, Pax6, c-Maf, E-cadherin and α-, β- and γ-crystallins. Therefore, while signaling by FGF receptors is essential for lens fiber differentiation, different FGF receptors function redundantly.