Thermolytic release of covalently linked DNA oligonucleotides and their conjugates from controlled-pore glass at near neutral pH

The functionalization of long chain alkylamine controlled-pore glass (CPG) with a 3-hydroxypropyl-(2-cyanoethyl)thiophosphoryl linker and its conversion to the support 7 has led to the synthesis of DNA oligonucleotides and their 3'- or (3',5')-conjugates. Indeed, CPG support 7 has been successfully employed in the synthesis of both native and fully phosphorothioated DNA 20-mers. Unlike conventional succinylated CPG supports, this distinctively functionalized support allows oligonucleotide deprotection and removal of the deprotection side products to proceed without releasing the oligonucleotide into the aqueous milieu. When freed from deprotection side products, the DNA oligonucleotide is thermolytically released from the support within 2 h under nearly neutral conditions (pH 7.2, 90 degrees C). The quality of these oligonucleotides is comparable to that of identical oligonucleotides synthesized from succinylated CPG supports in terms of shorter than full length oligonucleotide contaminants and overall yields. The versatility of the thermolytic CPG support 7 is further demonstrated by the synthesis of a DNA oligonucleotide (20-mer) and its conjugation with an azido and alkynyl groups at both 5'-and 3'-termini, respectively. The functionality of the (3',5')-heteroconjugated oligonucleotide 18 is verified by its circularization to the DNA oligonucleotide 19 under "click" chemistry conditions.     

Importance of the N-distal AP-2 binding element in Nef for simian immunodeficiency virus replication and pathogenicity in rhesus macaques

Point mutations in SIVmac239 Nef disrupting CD4 downmodulation and enhancement of virion infectivity attenuate viral replication in acutely infected rhesus macaques, but changes selected later in infection fully restore Nef function (A. J. Iafrate et al., J. Virol. 74:9836-9844, 2000). To further evaluate the relevance of these Nef functions for viral persistence and disease progression, we analyzed an SIVmac239 Nef mutant containing a deletion of amino acids Q64 to N67 (delta64-67Nef). This mutation inactivates the N-distal AP-2 clathrin adaptor binding element and disrupts the abilities of Nef to downregulate CD4, CD28 and CXCR4 and to stimulate viral replication in vitro. However, it does not impair the downmodulation of CD3 and class I major histocompatibility complex (MHC-I) or MHC-II and the upregulation of the MHC-II-associated invariant chain, and it has only a moderate effect on the enhancement of virion infectivity. Replication of the delta64-67Nef variant in acutely infected macaques was intermediate between grossly nef-deleted and wild-type SIVmac239. Subsequently, three of six macaques developed moderate to high viral loads and developed disease, whereas the remaining animals efficiently controlled SIV replication and showed a more attenuated clinical course of infection. Sequence analysis revealed that the deletion in nef was not repaired in any of these animals. However, some changes that slightly enhanced the ability of Nef to downmodulate CD4 and moderately increased Nef-mediated enhancement of viral replication and infectivity in vitro were observed in macaques developing high viral loads. Our results imply that both the Nef functions that were disrupted by the delta64-67 mutation and the activities that remained intact contribute to viral pathogenicity.     

Fluorescence methods (VistaCam iX proof and DIAGNODent pen) for the detection of occlusal carious lesions in teeth recovered from archaeological context

Diagnosis of occlusal enamel caries in archaeologically derived collections remains a controversial problem because the accumulation of contaminants in fissures can interfere with diagnosis. Certain novel light‐induced fluorescence methods, such as the DIAGNODent pen 2190 (DD) and VistaCam iX Proof (VC), have been used to detect dental caries in clinical settings. In this study, the abilities of DD and VC to detect initial enamel caries in archaeologically derived material is determined and compared with those of other methods (visual inspection, X‐ray, histology, and micro‐CT). Dental material encompassing the remains of 58 individuals, including a total of 380 teeth from each of three historical periods: modern Islamic (AD 1850–1950), Islamic (AD 600–1200) and late Roman (AD 200–400), obtained from two archaeological sites (Terqa and Tell Masaikh) located in the Middle Euphrates valley (Syria), were analyzed. VC was found to have excellent sensitivity (98), while DD obtained lower sensitivity (76) in detecting dental caries in its early stages. The results obtained by VC and micro‐CT, considered the most reliable imaging technique, were not statistically significant (P = 0.3068). By contrast, results obtained by DD and micro‐CT results, and DD and VC results were statistically significant (P < 0.0001, P = 0.0015, respectively). However the presence of dirt, stain, calculus, and plaque in the pits and fissures of the occlusal surface compromise correct diagnosis of caries by VC and DD. Consequently, for teeth recovered from archaeological contexts where staining, calculus and plaque are present, the best solution remains micro‐CT. Am J Phys Anthropol 154:525–534, 2014. © 2014 Wiley Periodicals, Inc.     

SEXUAL SELECTION COUNTERACTS EXTINCTION OF SMALL POPULATIONS OF THE BULB MITES

Genetic drift in small populations can increase frequency of deleterious recessives and consequently lead to inbreeding depression and population extinction. On the other hand, as homozygosity at deleterious recessives increases, they should be purged from populations more effectively by selection. Sexual selection has been postulated to strengthen selection against deleterious mutations, and should thus decrease extinction rate and intensify purging of inbreeding depression. We tested these predictions in the bulb mite Rhizoglyphus robini. We created 100 replicate lines of small populations (five males and five females) and in half of them experimentally removed sexual selection by enforcing monogamy. The lines were propagated for eight generations and then assayed for purging of inbreeding depression. We found that proportion of lines which went extinct was lower with sexual selection than without. We also found evidence for purging of inbreeding depression in the lines with sexual selection, but not in lines without sexual selection. Our results suggest that purging of inbreeding depression was more effective against mutations with relatively large deleterious effects. Thus, although our data clearly indicate a positive impact of sexual selection on short‐term survival of bottlenecked populations, long‐term consequences are less clear as they may be negatively impacted by accumulation of deleterious mutations of small effect.     

UHPLC method for the simultaneous determination of β-blockers, isoflavones and their metabolites in human urine

A rapid-resolution ultra high-performance liquid chromatography separation method (UHPLC) for the simultaneous determination of the following β-blockers: milrinone, sotalol, metoprolol, propranolol and carvedilol, and their metabolites: 5′-hydroxylphenyl-carvedilol, O-desmethylcarvedilol, 4-hydroxypropranolol, α-hydroxy-metoprolol, O-desmethyl-metoprolol; the following isoflavones: genistein, daidzein, glycitin, glycitein, puerarin and biochanin A; as well as their metabolites: dihydrogenistein, desmethylglycitein, 8-hydroxygenistein, daidzein-7,4′-diglucoside, 8-hydroxydaidzein, dihydrobiochanin A in human urine was optimized. The analysed compounds were extracted from human urine by means of solid phase extraction (SPE). The effective UHPLC separation of the examined compounds was applied on a Hypersil GOLD? (50 mm × 2.1 mm, 1.9 μm) column with a gradient mobile phase system and a UV detector. The complete separation of all analytes was achieved within 8.0 min. The method was validated for the determination of the aforementioned substances in human urine. The linear ranges, limits of detection (LOD) and limits of quantification (LOQ) for β-blockers, isoflavones and their metabolites were determined. The intra- and inter-day precision (%C.V.) was less than 4.48%, and the intra-day and inter-day accuracy was less than 4.74%. The tested SPE sorbent proved that appropriate absolute recoveries can be obtained for Oasis HLB (Waters). The mean recovery of the analytes, using the new SPE procedure, amounted from 70.14% to 99.85%. The present paper reports, for the first time, the method for the determination of β-blockers, isoflavones and their metabolites in human urine samples. The newly developed method was suitably validated and successfully applied for the analysis of the certain of the aforementioned analytes in human urine samples obtained from the patients suffering cardiovascular disease.     

Catalase-peroxidase KatG of Burkholderia pseudomallei at 1.7A resolution

The catalase-peroxidase encoded by katG of Burkholderia pseudomallei (BpKatG) is 65% identical with KatG of Mycobacterium tuberculosis, the enzyme responsible for the activation of isoniazid as an antibiotic. The structure of a complex of BpKatG with an unidentified ligand, has been solved and refined at 1.7A resolution using X-ray synchrotron data collected from crystals flash-cooled with liquid nitrogen. The crystallographic agreement factors R and R(free) are 15.3% and 18.6%, respectively. The crystallized enzyme is a dimer with one modified heme group and one metal ion, likely sodium, per subunit. The modification on the heme group involves the covalent addition of two or three atoms, likely a perhydroxy group, to the secondary carbon atom of the vinyl group on ring I. The added group can form hydrogen bonds with two water molecules that are also in contact with the active-site residues Trp111 and His112, suggesting that the modification may have a catalytic role. The heme modification is in close proximity to an unusual covalent adduct among the side-chains of Trp111, Tyr238 and Met264. In addition, Trp111 appears to be oxidized on C(delta1) of the indole ring. The main channel, providing access of substrate hydrogen peroxide to the heme, contains a region of unassigned electron density consistent with the binding of a pyridine nucleotide-like molecule. An interior cavity, containing the sodium ion and an additional region of unassigned density, is evident adjacent to the adduct and is accessible to the outside through a second funnel-shaped channel. A large cleft in the side of the subunit is evident and may be a potential substrate-binding site with a clear pathway for electron transfer to the active-site heme group through the adduct.