Interaction of human papillomavirus (HPV) type 16 capsid proteins with HPV DNA requires an intact L2 N-terminal sequence.

Encapsidation of papillomavirus DNA involves DNA-protein and protein-protein interactions. We sought to define the role of each human papillomavirus (HPV) capsid protein in HPV DNA encapsidation. HPV16 major (L1) and minor (L2) capsid proteins purified from recombinant vaccinia virus-infected cells were compared for their ability to bind nucleic acids. L2 protein, but not L1 protein, could bind HPV DNA. To map the DNA-binding region of L2, a series of truncated or point-mutated L2 protein open reading frames were used to show that only the N terminal of L2 was required for L2-DNA binding. This interaction depends critically on charged amino acids (Lys or Arg) in the first 12 amino acids of the N terminal of the protein. Several techniques were used to show that L2 interaction with DNA did not require specific DNA sequences. We propose that HPV L2 protein may play a major role in papillomavirus capsid assembly by introducing HPV DNA to the virus particles formed by the self assembly of the L1 major structural protein.     

Helical motion analysis of the knee--II. Kinematics of uninjured and injured knees during walking and pivoting

The knee kinematics of eight individuals with uninjured knees and of seven individuals with ruptured anterior cruciate ligaments have been investigated during walking and pivoting. The kinematics were measured using a six degree of freedom goniometer and quantitated using helical motion analysis. The helical motion variables reveal clearly that the knee is definitely neither a hinge nor a planar joint and its dynamic behavior changes over the stride. Ligamentous loss results in more adduction and external rotation during certain periods of the stride. Also, the range of translation of the tibia in the medial/lateral direction is reduced, and its average translation is more medial.     

Trichothecene mycotoxins in aerosolized conidia of Stachybotrys atra

Stachybotrys atra is the etiologic agent of stachybotryotoxicosis, and this fungus and its trichothecene mycotoxins were recently implicated in an outbreak of unexplained illness in homes. S. atra was grown on sterile rice, autoclaved, dried, and then aerosolized by acoustic vibration. The distribution of particles (mass and number) was monitored on an aerodynamic particle sizer interfaced with a computer. Dust was collected on preweighed glass-fiber filters and extracted with 90% aqueous methanol. Extracts were tested for the ability to inhibit protein synthesis in rat alveolar macrophages, the ability to inhibit the proliferation of mouse thymocytes, and the presence of specific trichothecene mycotoxins. Virtually all of the particles were less than 15 micron in aerodynamic diameter, and the mass median diameter was 5 micron. Thus, most of the particles were respirable. Microscopic analysis of the generated dust revealed that ca. 85% of the dust particles were conidia of S. atra, another 6% were hyphal fragments, and the remainder of the particles were unidentifiable. Thus, greater than 90% of the particles were of fungal origin. The extracts strongly inhibited protein synthesis and thymocyte proliferation. Purified satratoxin H was also highly toxic in the same systems. Each of the individual filters contained satratoxin H (average, 9.5 ng/mg of dust). Satratoxin G and trichoverrols A and B were found in lesser amounts in some, but not all, of the filters. The limit of analysis is ca. 50 ng. These results establish that the conidia of S. atra contain trichothecene mycotoxins. In view of the potent toxicity of the trichothecenes, the inhalation of aerosols containing high concentrations of these conidia could be a potential hazard to health.     

Enzymatic aryl-o-methyl-C labeling of model lignin monomers

Aryl-O-methyl ethers are abundant in aerobic and anaerobic environments. In particular, lignin is composed of units of this type. Lignin monomers specifically radiolabeled in methoxy, side chain, and ring carbons have been synthesized by chemical procedures and are important in studies of lignin synthesis and degradation, humus formation, and microbial O-demethylation. In this paper attention is drawn to an enzymatic procedure for preparing O-methyl-C-labeled aromatic lignin monomers which has not previously been exploited in microbial ecology and physiology studies and which has several advantages compared with chemical synthesis procedures. O-[methyl-C]vanillic and O-[methyl-C]ferulic acids were prepared with S-[methyl-C]adenosyl-l-methionine as the methyl donor, using commercially obtained porcine liver catechol-O-methyltransferase (EC 2.1.1.6). The specific activity of the methylated products was the same as that of the methyl donor, a maximum of about 58 muCi/mumol, and the yields were 42% (vanillate) and 35% (ferulate). Thus lignin monomers are readily prepared as O-methylated products of the catechol-O-methyltransferase reaction and, with this enzyme method of preparation, would be more widely available than labeled compounds which require chemical synthesis.     

The fate of lignin and lignin‐derived compounds in anaerobic environments

During ODP Leg 201 microbial communities in Eastern Equatorial Pacific Ocean and Peru Margin sediments were investigated. The sediment layers sampled extended down to 420 m below the sea floor, with estimated ages of up to 40 million years. Contamination-free anoxic slurries were inoculated into media containing different substrate combinations, all at micromolar concentration. These culture media were designed for a broad spectrum of physiological groups. A total of 162 pure cultures were isolated that could be grouped into 19 different phylotypes based on 16S rRNA gene analysis. The isolates belonged to the Alpha-, Gamma- and Deltaproteobacteria, the Firmicutes, Actinobacteria, and Bacteroidetes. The genera most frequently isolated were Bacillus (68 isolates) and Rhizobium (40 isolates). Comparison of strains with the same phylotypes by enterobacterial repetitive intergenic consensus (ERIC-PCR) analysis revealed the presence of several subgroups that did not correlate with medium, sediment depth or sampling site. The majority of the isolates, although obtained from anoxic environments and isolated under strictly anoxic conditions, turned out to be facultativly aerobic. Physiologically, the isolates were characterized as generalists, able to utilize a broad variety of electron donors with either oxygen, nitrate and in some cases manganese oxides as electron acceptors. The diversity inferred from physiological tests was even higher than that on the phylogenetic or genomic level. The outcome of the contamination tests, the isolation of close relatives of already known subsurface bacteria, the repeated finding of the same phylotype from different sites and the level of diversity present in the culture collection strongly suggest that indigenous deep-biosphere bacteria had been isolated.     

A covering method for detecting genetic associations between rare variants and common phenotypes

Genome wide association (GWA) studies, which test for association between common genetic markers and a disease phenotype, have shown varying degrees of success. While many factors could potentially confound GWA studies, we focus on the possibility that multiple, rare variants (RVs) may act in concert to influence disease etiology. Here, we describe an algorithm for RV analysis, RareCover. The algorithm combines a disparate collection of RVs with low effect and modest penetrance. Further, it does not require the rare variants be adjacent in location. Extensive simulations over a range of assumed penetrance and population attributable risk (PAR) values illustrate the power of our approach over other published methods, including the collapsing and weighted-collapsing strategies. To showcase the method, we apply RareCover to re-sequencing data from a cohort of 289 individuals at the extremes of Body Mass Index distribution (NCT00263042). Individual samples were re-sequenced at two genes, FAAH and MGLL, known to be involved in endocannabinoid metabolism (187Kbp for 148 obese and 150 controls). The RareCover analysis identifies exactly one significantly associated region in each gene, each about 5 Kbp in the upstream regulatory regions. The data suggests that the RVs help disrupt the expression of the two genes, leading to lowered metabolism of the corresponding cannabinoids. Overall, our results point to the power of including RVs in measuring genetic associations.     

The geographic distribution of reef and oceanic manta rays (Mobula alfredi and Mobula birostris) in Australian coastal waters

The known distribution of manta rays in Australian waters is patchy, with records primarily centred around tourism hotspots. We collated 11,614 records of Mobula alfredi from photo-ID databases (n = 10,715), aerial surveys (n = 378) and online reports (n = 521). The study confirms an uninterrupted coastal distribution from north of 26°S and 31°S on the west and east coasts, respectively. More southerly M. alfredi records relate to warm-water events with a southernmost extent at 34°S. Coastal sightings of Mobula birostris were rare (n = 32), likely reflecting a preference for offshore waters, but encompass a wider latitudinal extent than M. alfredi of 10–40°S.