Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins

The geometries of aromatic-aromatic interactions between phenylalanine residues in proteins are analysed in detail and correlated with energy calculations. A new definition of the interplanar angle is important for distinguishing favourable edge-to-face and unfavourable face-to-face orientations. The experimental observations are scattered over a wide range of conformational space, with no strongly preferred single orientation. However, Phe-Phe interactions occur almost exclusively in electrostatically attractive geometries: electrostatically unfavourable regions are only sparsely populated. Electrostatics dominate the geometry of interaction, while van der Waals' interactions are less significant, probably due to the hydrophobic environment of the protein core. The observations on proteins support the Hunter-Sanders rules for pi-pi interactions. In particular, offset stacked geometries, which theory predicts to be favourable, are observed experimentally. For monocyclic aromatics, use of a C-H dipole, the approach used in molecular mechanics calculations, accounts well for these aromatic-aromatic interactions. Comparison with the results obtained from the small molecules database indicates that the protein and small molecule crystal environments are very different.

Selective activation of AMPK-PGC-1alpha or PKB-TSC2-mTOR signaling can explain specific adaptive responses to endurance or resistance training-like electrical muscle stimulation

Endurance training induces a partial fast-to-slow muscle phenotype transformation and mitochondrial biogenesis but no growth. In contrast, resistance training mainly stimulates muscle protein synthesis resulting in hypertrophy. The aim of this study was to identify signaling events that may mediate the specific adaptations to these types of exercise. Isolated rat muscles were electrically stimulated with either high frequency (HFS; 6x10 repetitions of 3 s-bursts at 100 Hz to mimic resistance training) or low frequency (LFS; 3 h at 10 Hz to mimic endurance training). HFS significantly increased myofibrillar and sarcoplasmic protein synthesis 3 h after stimulation 5.3- and 2.7-fold, respectively. LFS had no significant effect on protein synthesis 3 h after stimulation but increased UCP3 mRNA 11.7-fold, whereas HFS had no significant effect on UCP3 mRNA. Only LFS increased AMPK phosphorylation significantly at Thr172 by approximately 2-fold and increased PGC-1alpha protein to 1.3 times of control. LFS had no effect on PKB phosphorylation but reduced TSC2 phosphorylation at Thr1462 and deactivated translational regulators. In contrast, HFS acutely increased phosphorylation of PKB at Ser473 5.3-fold and the phosphorylation of TSC2, mTOR, GSK-3beta at PKB-sensitive sites. HFS also caused a prolonged activation of the translational regulators p70 S6k, 4E-BP1, eIF-2B, and eEF2. These data suggest that a specific signaling response to LFS is a specific activation of the AMPK-PGC-1alpha signaling pathway which may explain some endurance training adaptations. HFS selectively activates the PKB-TSC2-mTOR cascade causing a prolonged activation of translational regulators, which is consistent with increased protein synthesis and muscle growth. We term this behavior the "AMPK-PKB switch." We hypothesize that the AMPK-PKB switch is a mechanism that partially mediates specific adaptations to endurance and resistance training, respectively.

The epidemiology of rhegmatogenous retinal detachment: geographical variation and clinical associations

AIMS/BACKGROUND

Rhegmatogenous retinal detachment (RRD) is a potentially blinding condition. Obtaining an accurate estimate of RRD incidence in the population is essential in understanding the healthcare burden related to this disorder.

METHODS

A systematic review of all population-based epidemiology studies of RRD published between January 1970 and January 2009 from Medline database searches was performed.

RESULTS

RRD incidence demonstrates significant geographical variation and its incidence has been reported to be between 6.3 and 17.9 per 100,000 population. For studies with a sample size >300 the median annual incidence per 100,000 population was 10.5 (IQR 8.1-13.2) and the mean proportion of bilateral RRD was 7.26%. Overall, the mean prevalence of lattice degeneration was 45.7+/-20.3% and myopia was 47.28+/-12.59%.

CONCLUSIONS

Estimates of RRD incidence have varied threefold, but inclusion criteria and other design features have differed across studies making direct comparisons difficult. The overall incidence of RRD is not yet well established: more incidence studies of adequate methodology are needed to explore temporal changes in incidence. RRD incidence varies with ethnicity and is strongly associated with increasing age, myopia and certain vitreo-retinal degenerations. Due to changes in cataract surgery trends, the proportion of pseudophakic RRD presenting to specialised centres appears to be increasing.

Induction of spermatogenesis by androgens in gonadotropin-deficient (hpg) mice

Using a new experimental model for studying the hormonal induction of spermatogenesis, the hpg mouse, which has congenital functional gonadotropin deficiency due to a major deletion in the GnRH gene, we investigated the roles of testosterone (T) and dihydrotestosterone (DHT) in the initiation of spermatogenesis. Weanling homozygous hpg male mice were implanted subdermally with SILASTIC brand implants of varying lengths (0-2 cm) filled with T or DHT, using phenotypically normal (N/N or N/hpg) and untreated hpg/hpg mice as positive and negative controls. After 8 weeks, both T and DHT equally stimulated (approximately 14-fold) testis size and induced qualitatively complete spermatogenesis despite low intratesticular androgen levels and undetectable circulating FSH. Stereological quantitation of Sertoli and germ cells demonstrated a dose-dependent rise in the absolute numbers of all germ cell types induced by both T and DHT. At maximal androgen doses, germ cell numbers expressed per Sertoli cell and homogenization-resistant elongated spermatids expressed per mg testis were increased to more than 80% of non-hpg control values. An in vitro fertilization assay confirmed that both T and DHT induced quantitatively normal fertilizing capacity of the sperm in hpg males. We conclude that androgens, acting through the androgen receptor without need for aromatization, initiate qualitatively complete spermatogenesis in the mouse, including fertile sperm despite low intratesticular androgen levels and the absence of blood FSH levels. The hpg mouse model is a useful new paradigm to study the molecular basis of the hormonal induction of spermatogenesis.

Global modulation of cellular transcription by human cytomegalovirus is initiated by viral glycoprotein B

Human cytomegalovirus (HCMV) infection alters the expression of many cellular genes, including IFN-stimulated genes (ISGs) [Zhu, H., Cong, J.-P., Mamtora, G., Gingeras, T. & Shenk, T. (1998) Proc. Natl. Acad. Sci. USA 95, 14470-14475]. By using high-density cDNA microarrays, we show that the HCMV-regulated gene expression profile in fibroblasts does not differ substantially from the response generated by IFN. Furthermore, we identified the specific viral component triggering this response as the envelope glycoprotein B (gB). Cells treated with gB, but not other herpesviral glycoproteins, exhibited the same transcriptional profile as HCMV-infected cells. Thus, the interaction of gB with its as yet unidentified cellular receptor is the principal mechanism by which HCMV alters cellular gene expression early during infection. These findings highlight a pioneering paradigm for the consequences of virus-receptor interactions.

Bifidobacterium longum, a lactic acid-producing intestinal bacterium inhibits colon cancer and modulates the intermediate biomarkers of colon carcinogenesis

The human colon can be described as a complex microbial ecosystem, comprising several hundred bacterial species. Some of these enteric bacteria are beneficial to the host and have been shown to exert antimutagenic and anticarcinogenic properties. We have investigated the colon tumor inhibitory activity of Bifidobacterium longum, a lactic acid-producing enterobacterium. The modifying effects of this lactic culture on colonic mucosal and/or tumor cell proliferation, ODC activity and ras-p21 oncoprotein expression in colon carcinogenesis were also analyzed. Male F344 rats were fed a modified AIN-76A diet containing 0 or 2% lyophilized cultures of B. longum and s.c. administered azoxymethane (AOM) dissolved in normal saline at a dose of 15 mg/kg body wt, once weekly for 2 weeks. Vehicle controls received an equal volume of normal saline s.c. Animals were maintained on control or experimental diets until termination of the study. Animals intended for analysis of cell proliferation were killed 20 weeks after the second AOM injection, whereas animals intended for colon tumor analysis and measurement of ODC activity and ras-p21 expression were killed 40 weeks after the last AOM injection. The data demonstrate that dietary administration of lyophilized cultures of B. longum resulted in significant suppression of colon tumor incidence and tumor multiplicity and also reduced tumor volume. Results also revealed that ingestion of B. longum significantly inhibited AOM-induced cell proliferation, ODC activity and expression of ras-p21 oncoprotein. Data suggest that oral administration of probiotic B. longum exerts strong antitumor activity, as indicated by modulation of the intermediate biomarkers of colon cancer, and consequently reduced tumor outcome.

Augmented digestion of lignocellulose by steam explosion, acid and alkaline pretreatment methods: a review

Lignocellulosic materials can be explored as one of the sustainable substrates for bioethanol production through microbial intervention as they are abundant, cheap and renewable. But at the same time, their recalcitrant structure makes the conversion process more cumbersome owing to their chemical composition which adversely affects the efficiency of bioethanol production. Therefore, the technical approaches to overcome recalcitrance of biomass feedstock has been developed to remove the barriers with the help of pretreatment methods which make cellulose more accessible to the hydrolytic enzymes, secreted by the microorganisms, for its conversion to glucose. Pretreatment of lignocellulosic biomass in cost effective manner is a major challenge to bioethanol technology research and development. Hence, in this review, we have discussed various aspects of three commonly used pretreatment methods, viz., steam explosion, acid and alkaline, applied on various lignocellulosic biomasses to augment their digestibility alongwith the challenges associated with their processing.

SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups

Automated methods have been developed to determine the preferred packing arrangement between interacting protein groups. A suite of FORTRAN programs, SIRIUS, is described for calculating and analysing the geometries of interacting protein groups using crystallographically derived atomic co-ordinates. The programs involved in calculating the geometries search for interacting pairs of protein groups using a distance criterion, and then calculate the spatial disposition and orientation of the pair. The second set of programs is devoted to analysis. This involves calculating the observed and expected distributions of the angles and assessing the statistical significance of the difference between the two. A database of the geometries of the 400 combinations of side-chain to side-chain interaction has been created. The approach used in analysing the geometrical information is illustrated here with specific examples of interactions between side-chains, peptide groups and particular types of atom. At the side-chain level, an analysis of aromatic-amino interactions, and the interactions of peptide carbonyl groups with arginine residues is presented. At the atomic level the analyses include the spatial disposition of oxygen atoms around tyrosine residues, and the frequency and type of contact between carbon, nitrogen and oxygen atoms. This information is currently being applied to the modelling of protein interactions.

Emerging experimental therapeutics for bipolar disorder: insights from the molecular and cellular actions of current mood stabilizers

Bipolar disorder afflicts approximately 1-3% of both men and women, and is coincident with major economic, societal, medical, and interpersonal consequences. Current mediations used for its treatment are associated with variable rates of efficacy and often intolerable side effects. While preclinical and clinical knowledge in the neurosciences has expanded at a tremendous rate, recent years have seen no major breakthroughs in the development of novel types of treatment for bipolar disorder. We review here approaches to develop novel treatments specifically for bipolar disorder. Deliberate (ie not by serendipity) treatments may come from one of two general mechanisms: (1) Understanding the mechanism of action of current medications and thereafter designing novel drugs that mimics these mechanism(s); (2) Basing medication development upon the hypothetical or proven underlying pathophysiology of bipolar disorder. In this review, we focus upon the first approach. Molecular and cellular targets of current mood stabilizers include lithium inhibitable enzymes where lithium competes for a magnesium binding site (inositol monophosphatase, inositol polyphosphate 1-phosphatase, glycogen synthase kinase-3 (GSK-3), fructose 1,6-bisphosphatase, bisphosphate nucleotidase, phosphoglucomutase), valproate inhibitable enzymes (succinate semialdehyde dehydrogenase, succinate semialdehyde reductase, histone deacetylase), targets of carbamazepine (sodium channels, adenosine receptors, adenylate cyclase), and signaling pathways regulated by multiple drugs of different classes (phosphoinositol/protein kinase C, cyclic AMP, arachidonic acid, neurotrophic pathways). While the task of developing novel medications for bipolar disorder is truly daunting, we are hopeful that understanding the mechanism of action of current mood stabilizers will ultimately lead clinical trials with more specific medications and thus better treatments those who suffer from this devastating illness.

Biocomposite scaffolds containing chitosan/alginate/nano-silica for bone tissue engineering

Bone tissue engineering is a promising alternative method for treating bone loss by a combination of biomaterials and cells. In this study, we fabricated biocomposite scaffolds by blending chitosan (CS), alginate (Alg) and nano-silica (nSiO2), followed by freeze drying. The prepared scaffolds (CS/Alg, CS/Alg/nSiO2) were characterized by SEM, FT-IR and XRD analyses. In vitro studies such as swelling, biodegradation, biomineralization, protein adsorption and cytotoxicity were also carried out. The scaffolds possessed a well-defined porous architecture with pore sizes varying from 20 to 100 μm suitable for cell infiltration. The presence of nSiO2 in the scaffolds facilitated increased protein adsorption and controlled swelling ability. The scaffolds were biodegradable and the addition of nSiO2 improved apatite deposition on these scaffolds. There was no significant cytotoxicity effect of these CS/Alg/nSiO2 scaffolds towards osteolineage cells. Thus, these results indicate that CS/Alg/nSiO2 scaffolds may have potential applications for bone tissue engineering.

Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast

Unlike higher eukaryotes, where an inverse correlation has been generally observed between gene expression and methylation of CpG sites, the budding yeast Saccharomyces cerevisiae lacks DNA methylation. Gene regulatory mechanisms can function independently of DNA methylation in yeast, and yeast strains expressing foreign DNA methylases that modify adenine and CpG residues have been found to be viable. We have used such strains to determine whether the transcriptional status of genes can influence the level of their DNA methylation in vivo. Several genes were tested, for example, GAL1, -7, and -10, PHO5, HMRa and HML alpha, and STE2 and STE3. Surprisingly, we found that all the genes displayed severalfold more methylation in the expressed state as compared to the repressed state. This procedure serves as a novel in vivo probe for the chromatin structure of yeast and potentially for higher eukaryotes.

Potential of lactic streptococci to produce bacteriocin

A survey was made on the bacteriocin-producing potential of lactic streptococci. Bacteriocin-like activities were isolated and partially purified from about 5% of the 280 strains investigated. The frequency of production varied from about 1% in Streptococcus lactis subsp. diacetylactis to 9 and 7.5% in S. lactis and Streptococcus cremoris, respectively. Eight strains of S. cremoris produced bacteriocins which, on the basis of heat stability at different pH values and inhibitory spectrum, could be divided into four types. From 54 S. lactis strains, 5 strains produced inhibitory substances, namely, three nisin-like antibiotics and two different bacteriocins. Only 1 of 93 S. lactis subsp. diacetylactis strains produced a bacteriocin which was very similar to bacteriocins of type I in S. cremoris. All of the bacteriocins that were partially purified by ammonium sulfate precipitation showed very limited inhibitory spectra. Most of the lactic streptococci and a few members of the genera Clostridium, Leuconostoc, and Pediococcus were inhibited. None of the bacteriocins acted on gram-negative bacteria. The bacteriocinogenic strains were also characterized on the basis of plasmid content. All strains possessed between one and nine plasmids ranging from 1 to 50 megadaltons.

Effects of Momordica charantia fruit juice on islet morphology in the pancreas of the streptozotocin-diabetic rat

An investigation was made of the effect of Momordica charantia fruit juice on the distribution and number of alpha, beta and delta cells in the pancreas of streptozotocin (STZ)-induced diabetic rats using immunohistochemical methods. The results indicated that there was a significant (Student's t-test, P < 0.004) increase in the number of beta cells in M. charantia-treated animals when compared with untreated diabetics, however, their number was still significantly less than that obtained for normal rats. There was also a significant (P < 0.006) increase in the number of delta cells in STZ-diabetic rats compared to non-diabetic rats. This increase in the number of delta cells was not affected by M. charantia treatment. The number of alpha cells did not change significantly in M. charantia-treated rats when compared with untreated diabetic rats. Our results suggest that oral feeding of M. charantia fruit juice may have a role in the renewal of beta cells in STZ-diabetic rats or alternately may permit the recovery of partially destroyed beta cells.

Limited availability and higher cost of gluten-free foods

BACKGROUND

A gluten-free diet is the only treatment for patients with coeliac disease, although it can be burdensome to follow and result in inadequate nutrient intake. The cost and availability of a gluten-free diet has been cited as a cause of incomplete dietary compliance; however, this has not been extensively investigated. The aim was to investigate the availability and cost of gluten-free foods across a wide range of stores.

METHODS

The availability and cost of 20 foods (both wheat-based and everyday foods) was surveyed at 30 different stores across five different store categories. For each of the 20 foods, four products were selected (branded gluten-free, cheapest gluten-free, branded standard, cheapest standard) resulting in sampling of up to 80 products in each of the 30 stores.

RESULTS

In general, there was limited availability of gluten-free foods, with an average of 8.2 of the 20 (41%) foods being available in a gluten-free version per store. Regular supermarkets had a greater availability (18.0/20, 90%), whereas budget supermarkets (1.8/20, 9%) and corner shops (1.8/20, 9%) had almost no gluten-free versions (P < 0.001). All 10 gluten-free versions of wheat-based foods were more costly than their standard counterparts (76-518% more expensive; P < 0.001). Some gluten-free versions of everyday foods were also more costly than standard counterparts (2-124%).

CONCLUSIONS

There is limited availability of gluten-free foods and they are generally more expensive than their standard counterparts. This may impact on compliance to a gluten-free diet, with potential nutritional and clinical consequences, together with an increased risk of complications.

Intact mirror-tracing and impaired rotary-pursuit skill learning in patients with Huntington's disease: evidence for dissociable memory systems in skill learning

Skill learning in early-stage Huntington's disease (HD) patients was compared with that of normal controls on 2 perceptual-motor tasks, rotary pursuit and mirror tracing. HD patients demonstrated a dissociation between impaired rotary-pursuit and intact mirror-tracing skill learning. These results suggest that different forms of perceptual-motor skill learning are mediated by separable neural circuits. A striatal memory system may be essential for sequence or open-loop skill learning but not for skills that involve the closed-loop learning of novel visual-response mappings. It is hypothesized that working memory deficits in HD resulting from frontostriatal damage may account broadly for intact and impaired long-term learning and memory in HD patients.

Identification, cellular localization, isolation, and characterization of human Clara cell-specific 10 KD protein

Human lung lavage proteins were fractionated by centrifugation and molecular sieving. An antiserum to the post-albumin fraction of the soluble proteins reacted with a 10 KD protein and this protein was isolated by conventional chromatography. The protein, which has a pI of 4.8, consists of two 5 KD polypeptides and is rich in glutamic acid, leucine, serine, and aspartic acid amino acids. The protein does not bind to concanavalin A, pancreatic elastase, leukocyte elastase, or trypsin, and lacks anti-protease activity. It constitutes about 0.15% of the soluble proteins in lung lavage. Antibodies to the 10 KD protein specifically and exclusively stain Clara cells in human, dog, and rat. Staining of granules of Clara cells was prominent in the distal bronchioles; however, the non-ciliated cells of respiratory bronchioles did not stain for the 10 KD protein. This 10 KD protein appears in fetal lungs at 21 weeks of gestation, and was present in about 10% of the primary pulmonary adenocarcinomas. As a specific marker for Clara cells, this protein could be useful in the study of development, regulation of secretion, and pathobiology of these cells.

Pyruvate and related alpha-ketoacids protect mammalian cells in culture against hydrogen peroxide-induced cytotoxicity

Pyruvate efficiently protected V79 Chinese hamster cells against the lethal effects of hydrogen peroxide. Protection was also provided by other alpha-ketoacids, such as alpha-ketobutyrate, alpha-ketoglutarate and alpha-ketoadipate, although higher concentrations were required. The corresponding beta-ketoacids had no effect. The results indicate that pyruvate and other alpha-ketoacids possess antioxidant activity in vitro and, probably, in vivo.

Energy expenditure of Gambian women during peak agricultural activity measured by the doubly-labelled water method

The doubly-labelled water (2H218O) method was used to measure total energy expenditure (TEE) in ten non-pregnant, non-lactating (NPNL), six pregnant (P) and fourteen lactating (L) women in a rural Gambian community. Measurements were made on free-living subjects at a period of peak energetic stress when high agricultural work loads coincided with a hungary season to induce moderately severe negative energy balance. TEE averaged 10.42 (SD 2.08) MJ/d, equivalent to 1.95 (SD 0.38) times resting metabolic rate (RMR). The energy cost of physical activity plus thermogenesis, derived as TEE-RMR, averaged 4.94 (SD 1.96) MJ/d. Expressed per kg body-weight (103 kJ/kg per d) this component of expenditure was 2.5 times greater than comparative values from inactive, affluent women studied previously (39 kJ/kg per d). Estimated energy intake (EI) in a subset of the women (n 13) was only 4.80 (SD 1.58) MJ/d, yielding an apparent deficit of 6.08 MJ/d between EI and TEE. Weight changes suggested that endogenous fat oxidation accounted for only about 0.85 MJ/d, leaving an unexplained difference of over 5 MJ/d. Critical analysis of possible errors suggests that the new doubly-labelled water method has provided the most reliable estimates and that the estimates of EI were substantially in error. This finding has important consequences for other food intake studies.