DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis

The availability of sequences of entire genomes has dramatically increased the number of protein targets, many of which will need to be overexpressed in cells other than the original source of DNA. Gene synthesis often provides a fast and economically efficient approach. The synthetic gene can be optimized for expression and constructed for easy mutational manipulation without regard to the parent genome. Yet design and construction of synthetic genes, especially those coding for large proteins, can be a slow, difficult and confusing process. We have written a computer program that automates the design of oligonucleotides for gene synthesis. Our program requires simple input information, i.e. amino acid sequence of the target protein and melting temperature (needed for the gene assembly) of synthetic oligonucleotides. The program outputs a series of oligonucleotide sequences with codons optimized for expression in an organism of choice. Those oligonucleotides are characterized by highly homogeneous melting temperatures and a minimized tendency for hairpin formation. With the help of this program and a two-step PCR method, we have successfully constructed numerous synthetic genes, ranging from 139 to 1042 bp. The approach presented here simplifies the production of proteins from a wide variety of organisms for genomics-based studies.     

Defective isotype-specific regulation of IgA anti-erythrocyte autoantibody-forming cells in NZB mice

B cell hyperactivity characterizes many autoimmune diseases. In NZB mice this is manifested by a variety of immunologic aberrations, including increased B cell proliferation and hyper IgM and IgA secretion in vitro. Recent studies have shown that IgA secretion can be suppressed or enhanced in an isotype-specific manner by a soluble factor(s), called IgA-binding factor (IgABF), produced by IgA FcR-bearing T cells. We now show that T cells from young NZB mice, cultured with high concentrations of IgA, produce an IgABF that has aberrant biologic activity when compared to IgABF produced from IgA FcR+ T cells of BALB/c mice. Although BALB/c IgABF normally suppresses proliferation and secretion by IgA-producing B cells, neither proliferation nor IgA secretion from normal murine IgA-B cells is suppressed by NZB IgABF. In fact, IgA secretion is significantly enhanced by NZB IgABF. We also present the first evidence of IgA anti-mouse erythrocyte (anti-MRBC) autoantibody-forming cells present in the spleens of NZB mice. Whereas BALB/c IgABF suppresses the in vitro generation of IgA anti-MRBC autoantibody-forming cells by NZB spleen cells, NZB IgABF enhances this response. Of particular interest is the development of IgA anti-MRBC autoantibody-forming cells in cultures of spleen cells from nonautoimmune BALB/c mice in the presence of NZB IgABF. These studies suggest that isotype-specific T cells factors might play an important role in the development of autoantibody-forming cells.     

A test of two mechanisms proposed to optimize grassland aboveground primary productivity in response to grazing

Aims Mesic grasslands have a long evolutionary history of grazing by large herbivores and as a consequence, grassland species have numerous adaptations allowing them to respond favourably to grazing. Although empirical evidence has been equivocal, theory predicts that such adaptations combined with alterations in resources can lead to grazing-induced overcompensation in aboveground net primary production (ANPP; grazed ANPP> ungrazed ANPP) under certain conditions. We tested two specific predictions from theory. First, overcompensation is more likely to occur in annually burned grasslands because limiting nutrients that would be lost with frequent fires are recycled through grazers and stimulate ANPP. Second, overcompensation of biomass lost to grazers is more likely to occur in unburned sites where grazing has the greatest effect on increasing light availability through alterations in canopy structure.Methods We tested these nutrient versus light-based predictions in grazed grasslands that had been annually burned or protected from fire for>20 years. We assessed responses in ANPP to grazing by large ungulates using both permanent and moveable grazing exclosures (252 exclosures from which biomass was harvested from 3192 quadrats) in a 2-year study. Study sites were located at the Konza Prairie Biological Station (KPBS) in North America and at Kruger National Park (KNP) in South Africa. At KPBS, sites were grazed by North American bison whereas in KNP sites were grazed either by a diverse suite of herbivores (e.g. blue wildebeest, Burchell's zebra, African buffalo) or by a single large ungulate (African buffalo).Important findings We found no evidence for overcompensation in either burned or unburned sites, regardless of grazer type. Thus, there was no support for either mechanism leading to overcompensation. Instead, complete compensation of total biomass lost to grazers was the most common response characterizing grazing–ANPP relationships with, in some cases, undercompensation of grass ANPP being offset by increased ANPP of forbs likely due to competitive release. The capability of these very different grass-dominated systems to maintain ANPP while being grazed has important implications for energy flow, ecosystem function and the trophic dynamics of grasslands.     

Comparison of two ultracentrifugation procedures for separation of nonhuman primate lipoproteins.

A comparison of nonhuman primate plasma lipoproteins isolated by swinging bucket rotor density gradient or fixed angle rotor differential ultracentrifugation is described. Whereas these two methods produced comparable results for the composition of low density (LDL) and high density (HDL) lipoproteins, the very low density lipoprotein (VLDL) fraction isolated with the swinging-bucket rotor contained relatively more cholesterol (free and esterified) and less phospholipid and protein than that fraction obtained with the fixed-angle rotor. Estimations of lipoprotein concentration by agarose gel electrophoresis and particle size by electron microscopy coupled with molar ratios of surface to core constituents indicate that the swinging bucket procedure resulted in a more complete harvest of VLDL particles, especially those in the larger size range.     

Worker honey bee ovary development: seasonal variation and the influence of larval and adult nutrition

We examined the effect of larval and adult nutrition on worker honey bee (Apis mellifera L.) ovary development. Workers were fed high or low-pollen diets as larvae, and high or low-protein diets as adults. Workers fed low-protein diets at both life stages had the lowest levels of ovary development, followed by those fed high-protein diets as larvae and low- quality diets as adults, and then those fed diets poor in protein as larvae but high as adults. Workers fed high-protein diets at both life stages had the highest levels of ovary development. The increases in ovary development due to improved dietary protein in the larval and adult life stages were additive. Adult diet also had an effect on body mass. The results demonstrate that both carry-over of larval reserves and nutrients acquired in the adult life stage are important to ovary development in worker honey bees. Carry-over from larval development, however, appears to be less important to adult fecundity than is adult nutrition. Seasonal trends in worker ovary development and mass were examined throughout the brood rearing season. Worker ovary development was lowest in spring, highest in mid-summer, and intermediate in fall.     

Relative inefficiency of soluble recombinant CD4 for inhibition of infection by monocyte-tropic HIV in monocytes and T cells

Macrophages are major viral reservoirs in the brain, lungs, and lymph nodes of HIV-infected patients. But not all HIV isolates infect macrophages. The molecular basis for this restrictive target cell tropism and the mechanisms by which HIV infects macrophages are not well understood: virus uptake by CD4-dependent and -independent pathways have both been proposed. Soluble rCD4 (sCD4) binds with high affinity to gp 120, the envelope glycoprotein of HIV, and at relatively low concentrations (less than 1 microgram/ml) completely inhibits infection of many HIV strains in T cells or T cell lines. HTLV-IIIB infection of the H9 T cell line was completely inhibited by prior treatment of virus with 10 micrograms/ml sCD4: no p24 Ag or HIV-induced T cell syncytia were detected in cultures of H9 cells exposed to 1 x 10(4) TCID50 HTLV-IIIB in the presence of sCD4. Under identical conditions and at a 100-fold lower viral inoculum, 10 micrograms/ml sCD4 had little or no effect on infection of monocytes by any of six different HIV isolates by three different criteria: p24 Ag release, virus-induced cytopathic effects, and the frequency of infected cells that express HIV-specific mRNA. At 10- to 100-fold higher concentrations of sCD4, however, infection was completely inhibited. Monoclonal anti-CD4 also prevented infection of these same viral isolates in monocytes. The relative inefficiency of sCD4 for inhibition of HIV infection in monocytes was a property of the virion, not the target cell: HIV isolates that infect both monocytes and T cells required similarly high levels of sCD4 (100 to 200 micrograms/ml) for inhibition of infection. These data suggest that the gp120 of progeny HIV derived from macrophages interacts with sCD4 differently than that of virions derived from T cells. For both variants of HIV, however, the predominant mechanism of virus entry for infection is CD4-dependent.     

Effects of brown and turbid water on piscivore–prey fish interactions along a visibility gradient

1. Environmental changes such as eutrophication and increasing inputs of humic matter (brownification) may have strong effects on predator–prey interactions in lakes through a reduction in the visual conditions affecting foraging behaviour of visually oriented predators. 2. In this experiment, we studied the effects of visual range (25–200 cm) in combination with optically deteriorating treatments (algae, clay or brown humic water) on predator–prey interactions between pike (Esox lucius) and roach (Rutilus rutilus). We measured effects on reaction distance and strike distance for pike and escape distance for roach, when pike individuals were exposed to free‐swimming roach as well as to roach held in a glass cylinder. 3. We found that reaction distance decreased with decreasing visual range caused by increasing levels of algae, clay or humic matter. The effect of reaction distance was stronger in turbid water (clay, algae) than in the brown water treatment. 4. Strike distance was neither affected by visual range nor by optical treatment, but we found shorter strike distances when pike attacked roach using visual cues only (roach held in a cylinder) compared to when pike could use multiple senses (free‐swimming roach). Escape distance for roach was longer in turbid than in brown water treatments. 5. Changes in environmental drivers, such as eutrophication and brownification, affecting the optical climate should thus have consequences for the strength of predator–prey interactions through changes in piscivore foraging efficiency and prey escape behaviour. This in turn may affect lake ecosystems through higher‐order interactions.     

Hydrothermal treatment and iodine binding provide insights into the organization of glucan chains within the semi‐crystalline lamellae of corn starch granules

The importance of glucan chains that pass through both the amorphous and crystalline lamellae (tie chains) in the organization of corn starch granules was studied using heat‐moisture treatment (HMT), annealing (ANN), and iodine binding. Molecular structural analysis showed that hylon starches (HV, HVII, and HVIII) contained higher proportion of intermediate glucan chains (HVIII > HVII > HV) than normal corn (CN) starch. Wide angle X‐ray scattering revealed that on HMT, the extent of polymorphic transition in hylon starches decreased with increasing proportion of intermediate and long chains. Iodine treated hylon starches exhibited increased order in the V‐type polymorphism as evidenced by the intense peak at 20° 2θ and the strong reflection intensity at 7.5° 2θ and the extent of the change depended on the type of hylon starch. DSC results showed that the gelatinization enthalpy of CN and waxy corn starch (CW) remained unchanged after ANN. However, hylon starches showed a significant increase in enthalpy with more distinct endotherms after ANN. It can be concluded that tie chains influence the organization of crystalline lamellae in amylose extender mutant starches. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 871–885, 2014.