Small‐Molecule APOBEC3G DNA Cytosine Deaminase Inhibitors Based on a 4‐Amino‐1,2,4‐triazole‐3‐thiol Scaffold

APOBEC3G (A3G) is a single‐stranded DNA cytosine deaminase that functions in innate immunity against retroviruses and retrotransposons. Although A3G can potently restrict Vif‐deficient HIV‐1 replication by catalyzing excessive levels of G→A hypermutation, sublethal levels of A3G‐catalyzed mutation may contribute to the high level of HIV‐1 fitness and its incurable prognosis. To chemically modulate A3G catalytic activity with the goal of decreasing the HIV‐1 genomic mutation rate, we synthesized and biochemically evaluated a class of 4‐amino‐1,2,4‐triazole‐3‐thiol small‐molecule inhibitors identified by high‐throughput screening. This class of compounds exhibits low‐micromolar (3.9–8.2 μM ) inhibitory potency and remarkable specificity for A3G versus the related cytosine deaminase, APOBEC3A. Chemical modification of inhibitors, A3G mutational screening, and thiol reactivity studies implicate C321, a residue proximal to the active site, as the critical A3G target for this class of molecules.     

Optical Properties and Associated Hygroscopicity of Clay Aerosols

Airborne mineral dust particles contribute a significant fraction to the total aerosol mass, thus they make a substantial contribution to the Earth's radiative budget by direct scattering and absorption of radiation. Quantifying their contribution is complicated by the variability of optical properties as a function of water uptake. To improve understanding, we directly measured the relative humidity (RH) dependence of extinction [fRH_ext(RH, Dry)] for three key silicate clay components (illite, kaolinite, and montmorillonite) of mineral dust aerosols through cavity ring-down spectroscopy at 532 nm. The three clays studied show significant differences in fRH_ext(RH, Dry) at three RH values, and reasons for this are explored. With 68% RH as an example, we used the fRH_ext(RH, Dry) and Mie theory to calculate a growth factor for comparison with other measurement techniques. Humidified tandem differential mobility analyzer and quartz crystal microbalance growth factors from the literature are larger than our optical measurements indicate. An apparent decrease in particle size calculated from optical measurements for illite and kaolinite was further investigated by determining the aerosol electrical mobility size distribution of 68% RH and dry clay particles at that indicated shrinkage of approximately 10% at elevated humidity. Direct optical measurement has advantages because the effects of irregular shape and internal voids are observed. Our calculated growth factors provide a lower limit and can be incorporated into climate models in conjunction with other results to reduce the uncertainty associated with the optical response to water uptake on clay aerosols.     

Design and Characterization of a Fluidized Bed Aerosol Generator: A Source for Dry,Submicrometer Aerosol

A fluidized bed aerosol generator has been designed and built for the purpose of generating a constant output of dry, submicrometer particles with a large number density. The output of the fluidized bed for generating aerosol particles from dry soot powder has been characterized using a differential mobility analyzer and a condensation particle counter. The particle size distribution is bimodal, with a mode in the submicrometer diameter size range and a mode in the supermicrometer diameter size range. The larger diameter mode is fully separated from the smaller mode and can thus be easily removed from the aerosol flow using impaction techniques. The distribution in the submicrometer size range is nearly log-normal, with a count median diameter falling between 0.1 and 0.3 micrometers. A number density of greater than 10⁵ particles cm^-3 of soot particles in the submicrometer range can be produced, constant to within 25% (1 standard deviation) over a 4 h time period. The number density of particles produced in the submicrometer range was found to vary with the ratio of soot to bronze beads in the bed mixture, whether or not a feed system was used, and nitrogen flow rate through the fluidized bed and feed system.     

Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant

Constrained binding peptides (peptide aptamers) may serve as tools to explore protein conformations and disrupt protein-protein interactions. The quality of the protein scaffold, by which the binding peptide is constrained and presented, is of crucial importance. SQT (Stefin A Quadruple Mutant-Tracy) is our most recent development in the Stefin A-derived scaffold series. Stefin A naturally uses three surfaces to interact with its targets. SQT tolerates peptide insertions at all three positions. Peptide aptamers in the SQT scaffold can be expressed in bacterial, yeast and human cells, and displayed as a fusion to truncated pIII on phage. Peptides that bind to CDK2 can show improved binding in protein microarrays when presented by the SQT scaffold. Yeast two-hybrid libraries have been screened for binders to the POZ domain of BCL-6 and to a peptide derived from PBP2', specific to methicillin-resistant Staphylococcus aureus. Presentation of the Noxa BH3 helix by SQT allows specific interaction with Mcl-1 in human cells. Together, our results show that Stefin A-derived scaffolds, including SQT, can be used for a variety of applications in cellular and molecular biology. We will henceforth refer to Stefin A-derived engineered proteins as Scannins.     

Comparison of the bligh and dyer and folch methods for total lipid determination in a broad range of marine tissue

For many studies, it is important to measure the total lipid content of biological samples accurately. The Bligh and Dyer method of extraction was developed as a rapid but effective method for determining total lipid content in fish muscle. However, it is also widely used in studies measuring total lipid content of whole fish and other tissues. Although some investigators may have used modified Bligh and Dyer procedures, rarely have modifications been specified nor has their effectiveness been quantitatively evaluated. Thus, we compared this method with that of the classic Folch extraction in determining total lipid content of fish samples ranging from 0.5 to 26.6% lipid. We performed both methods as originally specified, i.e., using the chloroform/methanol/water ratios of 1:2:0.8 and 2:2:1.8 (before and after dilution, respectively) for Bligh and Dyer and of 8:4:3 for Folch, and with the initial solvent/sample ratios of (3+1):1 (Bligh and Dyer) and 20:1 (Folch). We also compared these with several other solvent/sample ratios. In samples containing <2% lipid, the results of the two methods did not differ. However, for samples containing >2% lipid, the Bligh and Dyer method produced significantly lower estimates of lipid content, and this underestimation increased significantly with increasing lipid content of the sample. In the highest lipid samples, lipid content was underestimated by up to 50% using the Bligh and Dyer method. However, we found a highly significant linear relationship between the two methods, which will permit the correction of reported lipid levels in samples previously analyzed using an unmodified Bligh and Dyer extraction. In the future, modifications to procedures and solvent/sample ratios should be described.     

Morphological,mechanical, and thermal characterization of biopolymer composites based on polylactide and nanographite platelets

This work focuses on development and optimization of polylactide (PLA) and nanographite platelets (NGP) based composites to display possible superior mechanical and improved thermal stability. Melt blending and dry mixing methods of fabrication were employed at temperature of 180°C. Different Loading fractions of NGP were incorporated into polymer matrix. Morphological evaluation techniques such as XRD and TEM were applied to determine the degree of dispersion of NGPs into PLA matrix. Mechanical properties were evaluated and correlated to structural morphologies of PLA/NGP composites. Thermal properties of composites were studied to examine possible changes in T_g, T_c, T_m, and percentage crystallinity of these composites. The effect of mixing was also explored through double extrusion of some samples. It was concluded that composites containing 3 wt% NGP showed optimum mechanical performance without any significant changes in the thermal characteristics. POLYM. COMPOS., 2012. © 2012 Society of Plastics Engineers     

Chemical Synthesis of A Pore‐Forming Antimicrobial Protein,Caenopore‐5, by Using Native Chemical Ligation at a Glu‐Cys Site

The 2014 report from the World Health Organization (WHO) on antimicrobial resistance revealed an alarming rise in antibiotic resistance all around the world. Unlike classical antibiotics, with the exception of a few species, no acquired resistance towards antimicrobial peptides (AMPs) has been reported. Therefore, AMPs represent leads for the development of novel antibiotics. Caenopore‐5 is constitutively expressed in the intestine of the nematode Caenorhabditis elegans and is a pore‐forming AMP. The protein (82 amino acids) was successfully synthesised by using Boc solid‐phase peptide synthesis and native chemical ligation. No γ‐linked by‐product was observed despite the use of a C‐terminal Glu‐thioester. The folding of the synthetic protein was confirmed by ¹H NMR spectroscopy and circular dichroism and compared with data recorded for recombinant caenopore‐5. The permeabilisation activities of the protein and of shortened analogues were evaluated.     

Differential Effects of Estrogen and Progestin on Apolipoprotein B100 and B48 Kinetics in Postmenopausal Women

The distinct effects of the estrogen and progestin components of hormonal therapy on the metabolism of apolipoprotein (apo) B‐containing lipoproteins have not been studied. We enrolled eight healthy postmenopausal women in a placebo‐controlled, randomized, double‐blind crossover study. Each subject received placebo, conjugated equine estrogen (CEE, 0.625 mg/day) and CEE plus medroxyprogesterone acetate (MPA, 2.5 mg/day) for 8 weeks in a randomized order, with a 4‐week washout between phases. Main outcomes were the fractional catabolic rate (FCR) and production rate (PR) of apo B100 in triglyceride‐rich lipoproteins (TRL), intermediate‐density lipoproteins (IDL) and low ‐density lipoprotein (LDL) and of apo B48 in TRL. Compared to placebo, CEE increased TRL apo B100 PR (p = 0.04). CEE also increased LDL apo B100 FCR (p = 0.02), but this effect was offset by a significant increase in LDL apo B100 PR (p = 0.04). Adding MPA to CEE negated the CEE effects resulting in no significant changes in TRL apo B100 PR and LDL apo B100 FCR and PR relative to placebo. Relative to placebo, during CEE there was a trend toward a reduction in plasma apo B48 concentrations and PR (p = 0.07 and p = 0.12, respectively). Compared with CEE, CEE + MPA significantly increased TRL apo B48 FCR (p = 0.02) as well as apo B48 PR (p = 0.01), resulting in no significant changes in apo B48 concentration. Estrogen and progestin have independent and opposing effects on the metabolism of the atherogenic apo B100‐ and apo B48‐containing lipoproteins.     

Orientation and Feeding Responses of the Pollen Beetle, Meligethes aeneus, to Candytuft, Iberis amara

The pollen beetle, Meligethes aeneus, which is an important pest of oilseed rape, Brassica napus, and turnip rape, B. rapa var. campestris, does not oviposit in all species of the Brassicaceae. The relationship between M. aeneus and candytuft, Iberis amara (Brassicacae), was investigated as part of chemical ecological studies into the development of control methods employing non-host-derived repellents. In choice and nonchoice feeding tests, M. aeneus completely rejected I. amara. However, in a field experiment using traps baited with flowering racemes of I. amara and B. napus, M. aeneus was attracted to both species. Gas chromatographic (GC) and GC-electroantennogram (GC-EAG) analyses indicated that the profiles of the floral volatiles of the two species are different. At least 12 compounds among the I. amara floral volatiles were detected by the M. aeneus antenna, and, of these, hexanoic acid, (E)-4,8-dimethyl-1,3,7-nonatriene and alpha-cedrene were not found among B. napus flower volatiles. Since M. aeneus is stimulated by floral volatiles to approach I. amara, but rejects it near, or at, the plant surface, I. amara does not produce repellents that could be used to manipulate M. aeneus. However, it may contain feeding deterrent(s) that could be used in "push-pull" control techniques or in the development of resistant brassicaceous crops.     

Modeling of ultrasonic processing

Curing of fiber‐reinforced thermoset polymer composites requires an elevated temperature to accelerate the crosslinking reaction and also hydrostatic pressure to consolidate the part and suppress the formation of voids. These processing conditions can be provided by autoclaves of appropriate size, but these are expensive and sometimes difficult to schedule. Ultrasonic debulking followed by oven cure is an attractive alternative to autoclave cure. In this technique a movable “horn” driven at ultrasonic frequency is applied to the surface of the uncured part. This generates pressure and at the same time produces heating by viscoelastic dissipation. The part can be debulked to net shape and staged through the action of the ultrasound. There are a large enough number of experimental parameters in ultrasonic debulking and staging to make purely empirical process optimization difficult, and this paper outlines numerical simulation methods useful in understanding and developing the process. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 1609–1615, 2004