Single molecule DNA origami nanoarrays with controlled protein orientation.

The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.

The futility of fertility research? Barriers to embryo research in New Zealand.

AIMS: Successive New Zealand Health Ministers have failed to approve guidelines for research using viable human embryos, which effectively places a blanket ban on all research that "uses" viable human embryos in this country. This includes research that aims to improve currently available reproductive technologies, illustrated by a failed application to ministerial ethics committees for a clinical research project investigating the efficacy of in vitro fertilisation procedures. However, no data currently exists describing the degree to which these restrictions are inhibiting reproductive research in this country. METHODS: We have conducted a qualitative survey of New Zealand researchers from 20 major academic, clinical and governmental institutes to qualify the impact these restrictions are having on New Zealand's research outputs. RESULTS: The results suggest dissatisfaction with the current guidelines, and the lack of guidance from the Ministry of Health and associated ethics committees regarding what constitutes embryo research and therefore what research can be performed. CONCLUSIONS: The lack of current guidelines regarding the use of embryos for research is restricting improvements to established reproductive technologies, and any future research. We suggest that the Minister of Health instructs ministerial advisory and ethics committees to review the current guidelines and to define the term "use of embryos".

Lessons for modern insulin development.

There have been many advances in insulin with a realistic possibility of mimicking nature to improve insulin replacement, with a view to achieving improved metabolic control. Lessons can be learnt from the evolution of insulin, insulin development, and new advances in technology. This may lead to fewer side effects of therapy resulting in a lower risk of hypoglycaemia and less weight gain, which could in turn could reduce long-term complications for people with diabetes.

Volumetric and dimensional analysis of the guinea pig inner ear.

The objective of this study was to provide accurate volumetric data on the fluid spaces and soft tissue in the guinea pig inner ear by measuring all histologic serial sections by means of Metamorph Imaging Software at 400x to 1,000x magnification. The total endolymph volume of the inner ear was 4.691 mm3, of which 1.501 mm3 was in the cochlea, 3.090 mm3 in the vestibular labyrinth, and 0.100 mm3 in the endolymphatic duct and sac. The total perilymph volume was 15.938 mm3, of which 8.867 mm3 was in the cochlea and 7.071 mm3 in the vestibular labyrinth. The volume of the organ of Corti per millimeter length increased toward the apex, but the volumes of the stria vascularis, spiral ligament, and spiral limbus decreased. The volume of the macula utriculi was larger than that of the macula sacculi. The measurement of the luminal surface area of the stria vascularis was 3.944 mm2, and that of the vestibular dark cells was 5.772 mm2.

Recognition of the lipoyl domain is the ultimate determinant of substrate channelling in the pyruvate dehydrogenase multienzyme complex.

Reductive acetylation of the lipoyl domain (E2plip) of the dihydrolipoyl acetyltransferase component of the pyruvate dehydrogenase multienzyme complex of Escherichia coli is catalysed specifically by its partner pyruvate decarboxylase (E1p), and no productive interaction occurs with the analogous 2-oxoglutarate decarboxylase (E1o) of the 2-oxoglutarate dehydrogenase complex. Residues in the lipoyl-lysine beta-turn region of the unlipoylated E2plip domain (E2plip(apo)) undergo significant changes in both chemical shift and transverse relaxation time (T(2)) in the presence of E1p but not E1o. Residue Gly11, in a prominent surface loop between beta-strands 1 and 2 in the E2plip domain, was also observed to undergo a significant change in chemical shift. Addition of pyruvate to the mixture of E2plip(apo) and E1p caused larger changes in chemical shift and the appearance of multiple cross-peaks for certain residues, suggesting that the domain was experiencing more than one type of interaction. Residues in both beta-strands 4 and 5, together with those in the prominent surface loop and the following beta-strand 2, appeared to be interacting with E1p, as did a small patch of residues centred around Glu31. The values of T(2) across the polypeptide chain backbone were also lower than in the presence of E1p alone, suggesting that E2plip(apo) binds more tightly after the addition of pyruvate. The lipoylated domain (E2plip(holo)) also exhibited significant changes in chemical shift and decreases in the overall T(2) relaxation times in the presence of E1p, the residues principally affected being restricted to the half of the domain that contains the lipoyl-lysine (Lys41) residue. In addition, small chemical shift changes and a general drop in T(2) times in the presence of E1o were observed, indicating that E2plip(holo) can interact, weakly but non-productively, with E1o. It is evident that recognition of the protein domain is the ultimate determinant of whether reductive acetylation of the lipoyl group occurs, and that this is ensured by a mosaic of interactions with the Elp.

Restricted motion of the lipoyl-lysine swinging arm in the pyruvate dehydrogenase complex of Escherichia coli.

The three lipoyl (E2plip) domains of the dihydrolipoyl acetyltransferase component of the pyruvate dehydrogenase (PDH) complex of Escherichia coli house the lipoyl-lysine side chain essential for active-site coupling and substrate channelling within the complex. The structure of the unlipoylated form of the innermost domain (E2plip(apo)) was determined by multidimensional NMR spectroscopy and found to resemble closely that of a nonfunctional hybrid domain determined previously [Green et al. (1995) J. Mol. Biol. 248, 328-343]. The domain comprises two four-stranded beta-sheets, with the target lysine residue residing at the tip of a type-I beta-turn in one of the sheets; the N- and C-termini lie close together at the opposite end of the molecule in the other beta-sheet. Measurement of (15)N NMR relaxation parameters and backbone hydrogen/deuterium (H/D) exchange rates reveals that the residues in and surrounding the lipoyl-lysine beta-turn in the E2plip(apo) form of the domain become less flexible after lipoylation of the lysine residue. This implies that the lipoyl-lysine side chain may not sample the full range of conformational space once thought. Moreover, reductive acetylation of the lipoylated domain (E2plip(holo) --> E2plip(redac)) was accompanied by large changes in chemical shift between the two forms, and multiple resonances were observed for several residues. This implies a change in conformation and the existence of multiple conformations of the domain on reductive acetylation, which may be important in stabilizing this catalytic intermediate.

Structural determinants of post-translational modification and catalytic specificity for the lipoyl domains of the pyruvate dehydrogenase multienzyme complex of Escherichia coli.

The lipoyl domains of the dihydrolipoyl acyltransferase (E2p, E2o) components of the pyruvate and 2-oxoglutarate dehydrogenase multienzyme complexes are specifically recognised by their cognate 2-oxo acid decarboxylase (E1p, E1o). A prominent surface loop links the first and second beta-strands in all lipoyl domains, close in space to the lipoyl-lysine beta-turn. This loop was subjected to various modifications by directed mutagenesis of a sub-gene encoding a lipoyl domain of Escherichia coli E2p. Deletion of the loop (four residues) rendered the domain incapable of reductive acetylation by E. coli E1p in the presence of pyruvate, but insertion of a new loop (six residues) corresponding to that in the E2o lipoyl domain partly restored this ability, albeit with a much lower rate. However, the modified domain remained unable to undergo reductive succinylation by E1o in the presence of 2-oxoglutarate. Additional exchange of the two residues on the C-terminal side of the loop (V14A, E15T) had no effect. Insertion of a different four-residue loop also restored a limited ability to undergo reductive acetylation, but still significantly less than that of the wild-type domain. Exchanging the residue on the N-terminal side of the lipoyl-lysine beta-turn in the E2p and E2o domains (G39T), both singly and in conjunction with the loop exchange, had no effect on the ability of the E2p domain to be reductively acetylated but did confer a slight increase in susceptibility to reductive succinylation. All mutant E2p domains, apart from that with the loop deletion (LD), were readily lipoylated in vitro by E. coli lipoate protein ligase A; the E2p LD mutant could be lipoylated only at a significantly lower rate. Likewise, this domain exhibited 1D and 2D NMR spectra characteristic of a partially folded protein, whereas the spectra of mutants with modified loops were similar to those of the wild-type domain. The surface loop is evidently important to the structural integrity of the domain and may help to stabilize the thioester bond linking the acyl group to the reduced lipoyl-lysine swinging arm as part of the catalytic mechanism. Recognition of the lipoyl domain by its partner E1 appears to be a complex process and not attributable to any single determinant on the domain.

Detection of total and hemolysin-producing Vibrio parahaemolyticus in shellfish using multiplex PCR amplification of tl, tdh and trh.

Vibrio parahaemolyticus is an important human pathogen which can cause gastroenteritis when consumed in raw or partially-cooked seafood. A multiplex PCR amplification-based detection of total and virulent strains of V. parahaemolyticus was developed by targeting thermolabile hemolysin encoded by tl, thermostable direct hemolysin encoded by tdh, and thermostable direct hemolysin-related trh genes. Following optimization using oligonucleotide primers targeting tl, tdh and trh genes, the multiplex PCR was applied to V. parahaemolyticus from 27 clinical, 43 seafood, 15 environmental, 7 strains obtained from various laboratories and 19 from oyster plants. All 111 V. parahaemolyticus isolates showed PCR amplification of the tl gene; however, only 60 isolates showed amplification of tdh, and 43 isolates showed amplification of the trh gene. Also, 18 strains showed amplification of the tdh gene, but these strains did not show amplification of the trh gene. However, one strain exhibited amplification for the trh but not the tdh gene, suggesting both genes need to be targeted in a PCR amplification reaction to detect all hemolysin-producing strains of this pathogen. The multiplex PCR approach was successfully used to detect various strains of V parahaemolyticus in seeded oyster tissue homogenate. Sensitivity of detection for all three target gene segments was at least between 10(1)-10(2) cfu per 10 g of alkaline peptone water enriched seeded oyster tissue homogenate. This high level of sensitivity of detection of this pathogen within 8 h of pre-enrichment is well within the action level (10(4) cfu per 1 g of shell stock) suggested by the National Seafood Sanitation Program guideline. Compared to conventional microbiological culture methods, this multiplex PCR approach is rapid and reliable for accomplishing a comprehensive detection of V. parahaemolyticus in shellfish.

Cysteine sulfinic acid decarboxylase mRNA abundance decreases in rats fed a high-protein diet.

The partitioning of cysteine metabolism between sulfate and taurine biosynthetic pathways may be regulated in part by the activity of cysteine sulfinic acid decarboxylase (CSAD). CSAD activity is repressed by high-protein feeding, and we have previously reported that changes in CSAD activity are correlated with changes in CSAD protein. We conducted experiments to determine the relative expression of CSAD mRNA in rats fed 18 or 60% casein diets. In rats fed a 60% casein diet for 1 wk, hepatic CSAD activity and CSAD protein were 16 and 36%, respectively, of the values measured in rats fed the 18% casein diet. CSAD mRNA abundance in rats fed the 60% casein diet was 14% of the CSAD mRNA abundance in rats fed an 18% casein diet. The time course of the change in CSAD activity and mRNA abundance was examined in rats fed 18 or 60% casein diets for 48 h. Within 6 h of switching rats to a 60% casein diet, CSAD activity was decreased by 20% and after 48 h, activity was decreased 47% compared to activity measured at baseline. CSAD mRNA abundance was decreased 54% within 12 h of feeding rats a high-protein diet and remained depressed at 48 h. In a parallel group of rats fed the 18% casein diet, CSAD activity and CSAD mRNA were not significantly different from baseline values at 48 h. The decreased expression of CSAD mRNA in rats fed a high-protein diet is consistent with decreases in both CSAD enzyme activity and CSAD protein. Our results suggest dietary protein may regulate CSAD at the level of mRNA.

Detection of microbial pathogens in shellfish with multiplex PCR.

Multiplex PCR amplification of uidA, cth, invA, ctx, and tl genes was developed enabling simultaneous detection in shellfish of Escherichia coli, an indicator of fecal contamination and microbial pathogens, Salmonella typhimurium, Vibrio vulnificus, V. cholerae, and V. parahaemolyticus, respectively. Each of the five pairs of oligonucleotide primers was found to support PCR amplifications of only its targeted gene. The optimized multiplex PCR reaction utilized a PCR reaction buffer containing 2.5 mM MgCl2 and primer annealing temperature of 55 degrees C. Oyster tissue homogenate seeded with these microbial pathogens was subjected to DNA purification by the Chelextrade mark 100 (BioRad) method. The sensitivity of detection for each of the microbial pathogens was

Detection of Giardia in environmental waters by immuno-PCR amplification methods.

Genomic DNA was extracted either directly from Giardia muris cysts seeded into environmental surface waters or from cysts isolated by immunomagnetic beads (IMB). A 0.171-kbp segment of the giardin gene was PCR-amplified following "direct extraction" of Giardia DNA from seeded Cahaba river water concentrate with moderate turbidity (780 JTU's), but DNA purified from seeded Colorado river water concentrates with high turbidity (2 x 10(5) JTUs) failed to amplify. However, if the cysts were first separated by the IMB approach from seeded Cahaba or Colorado river waters, and the DNA released by a freeze-boil Chelex(R)100 treatment, detection of G. muris by PCR amplification could be achieved at a sensitivity of 3 x 10(0) or 3 x 10(1) cysts/ml, respectively. If, however, the G. muris cysts used to seed even moderately turbid river waters (780 JTUs) were formalin treated (which is conventionally used for microscopic examination), neither direct extraction nor IMB purification methods yielded amplifiable DNA. Use of immunomagnetic beads to separate Giardia cysts from complex matrices of environmental surface waters followed by DNA release and PCR amplification of the target giardin gene improved the reliability of detection of this pathogen with the required sensitivity.

Calcium and vitamin D status of pregnant teenagers in Maiduguri, Nigeria.

This study investigates parameters related to calcium and bone metabolism by determining the concentrations of total calcium, 25-hydroxyvitamin D, 1,25-dihydroxyvitamin D, parathyroid hormone, and phosphorous in young pregnant women. The patient population was 30 pregnant Nigerian teenage women grouped by trimester (10 per group), 10 women immediately following delivery, and 21 healthy age-matched controls. On the basis of serum prealbumin levels, the general nutrition of the pregnant women was found to be significantly below that of the more privileged and better-educated nonpregnant controls. The mean total calcium concentration in sera of the third-trimester women was 8.83 mg/dL, which was significantly below that of the controls (9.77 mg/dL) and the first-trimester group (9.30 mg/dL). Despite the 10% to 15% decline in the serum level of total calcium during pregnancy, the parathyroid hormone level decreased markedly from 0.60 to 0.61 ng/mL in the first and second trimesters to 0.41 ng/mL in the third trimester. Serum vitamin D and 1,25-dihydroxyvitamin D levels in the second and third trimesters were within the normal range. These data indicate that toward the end of gestation, pregnant teenagers in northern Nigeria appear to become calcium deficient and do not exhibit the expected increase in serum parathyroid hormone levels normally seen in pregnant women.

Biodegradability and microbial activities during composting of poultry litter.

Poultry litter is composted to reduce odor and pathogens and to improve its quality as a soil amendment. Organic material, e.g., sawdust, is added to increase the C:N ratio to achieve optimum degradation of organic C and retention of N through microbial biomass formation. However, the relative biodegradabilities of the organic material in poultry litter and the amendment are usually not known. Furthermore, it is assumed that as microorganisms metabolize organic compounds and produce CO2, they increase in biomass and, therefore, retain N. In this study, bench-scale compost reactors were used to determine the relative contributions of poultry litter and of the amendment (sawdust) to the biodegradability of a compost mix. Approximately 29% of the volatiles lost from the poultry litter mix came from the sawdust. Fiber analyses revealed that only a small portion of cellulose was degraded. Although microbial subpopulations able to degrade selected macromolecules were present at varying levels, the overall level of microorganisms did not change markedly. Populations capable of degrading bacterial cell walls were present throughout the composting period, and microbiological assays indicated that inorganic nutrients were available to support limited microbial growth. These results suggest that N compounds and inorganic nutrients are recycled, rather than fixed during composting.

Detection of viable Vibrio cholerae by reverse-transcriptase polymerase chain reaction (RT-PCR).

The use of conventional PCR can amplify target DNA from both viable and nonviable cells of Vibrio cholera. Detection of only viable microbial pathogens in biological samples, especially clinical and food samples, is usually desired to ensure positive test results are associated with active agents, and not the remains of dead cells. Positive identifications caused by nonliving causative agents may lead to misguided decisions concerning the effectiveness of treatment, and whether patient treatment should be continued or whether the food should be discarded. Consequently, this work was directed toward development of a reverse-transcriptase polymerase chain reaction (RT-PCR)-based in vitro DNA amplification method, which specifically detects only viable cells. Total RNA from both viable and nonviable cells was purified by using a FastPrep Cell Disrupter ([symbol: see text]Bio 101/Savant) and FastRNA extraction reagents ([symbol: see text]Bio 101). The purified RNA was treated with DNase I (RNase-free) to avoid any amplification from the contaminating target DNA. An RT-PCR approach using this rapid and effective method for RNA purification showed amplification of the target mRNA only from the viable cells. The sensitivity of detection of viable cells of V. cholerae was > or = 10(3), which is well within the minimum number of cells (10(5)-10(6)) required for infection. The use of a reliable prokaryotic RNA extraction method followed by RT-PCR amplification of the target mRNA can be used for specific detection of viable microbial pathogen, such as V. cholerae.

Prospects for the genetic manipulation of dairy cattle: opportunities beyond BST.

The dairy industry, with regulatory approvals of recombinant chymosin and bovine somatotropin (BST), has been at the forefront of food and agricultural biotechnology. The commercial fate of these products is one of several factors that may affect the success of future genetic manipulations in dairy cattle and dairy products. Other factors include technical and reproductive constraints in cattle and the cost of producing transgenic cattle. Early applications of genetic manipulation in cattle, for reasons of cost recoupment, may favor production of heterologous proteins in milk for pharmaceutical and medical use. Such applications could benefit genetic modification of milk and milk proteins for food use by providing advance knowledge and experience in mammalian protein expression. Other research opportunity areas that could affect prospects for genetic manipulation of dairy cattle include genome mapping, metabolic pathways, growth and development, and cattle/microbe interactions.

Expression of a foreign gene in Chlamydomonas reinhardtii.

Genomic transformation of Chlamydomonas reinhardtii exposed to glass-bead abrasion was accomplished with a chimeric neomycin phosphotransferaseII (NPTII)-encoding gene (nos::npt) flanked by the nopaline synthase promoter and polyadenylation sequences obtained from the Ti plasmid of Agrobacterium tumefaciens. These sequences were in a plasmid (pGA482) which also contained gene nit1 encoding nitrate reductase of C. reinhardtii. Transformants were selected by their ability to grow on medium containing nitrate, and 52% of these was also resistant to kanamycin. Evidence for nos::npt expression includes: (1) hybridization with probes specific for npt, (2) demonstration of NPTII activity after electrophoresis of extracts, and (3) chromatographic identification of the reaction product of NPTII, kanamycin phosphate. The highly biased codon usage in Chlamydomonas does not preclude expression.

Norepinephrine inhibits rat pre-adipocyte proliferation.

Hormonal and neural status are major determinants for cellular growth. The purpose of this study was to assess the influence of the adrenergic hormones on pre-adipocyte growth in primary cell culture. Stromal-vascular cells were obtained from the inguinal pad of young rats and grown in culture for two weeks. Cells were exposed to norepinephrine (NE) during the proliferative phase of growth, labelled by [3H]-thymidine incorporation and then placed on a differentiation promoting medium. Adipocytes and stromal cells were separated using a density gradient, and [3H]-thymidine content was determined for both cell types. NE reduced [3H]-thymidine uptake indicating a reduction in pre-adipocyte proliferation. NE-induced inhibition of pre-adipocyte growth was blocked by the presence of propranolol, whereas phenoxybenzamine had no effect, thereby suggesting that NE-inhibition is through beta-adrenoceptors. Pre-adipocytes were treated with NE for varying lengths of time to investigate whether cells were desensitized to chronic beta-adrenergic stimulation. In addition, adenosine deaminase (ADA) was also applied to eliminate adenosine which may accumulate during NE stimulation. Neither the duration of NE exposure nor ADA treatment affected adrenergic control of adipocyte growth. These studies indicate that NE reduces pre-adipocyte proliferation and therefore may be an important negative regulatory component of adipocyte growth.