Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections.     

Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging

We have previously used cryo-electron tomography combined with sub-volume averaging and classification to obtain 3D structures of macromolecular assemblies in cases where a single dominant species was present, and applied these methods to the analysis of a variety of trimeric HIV-1 and SIV envelope glycoproteins (Env). Here, we extend these studies by demonstrating automated, iterative, missing wedge-corrected 3D image alignment and classification methods to distinguish multiple conformations that are present simultaneously. We present a method for measuring the spatial distribution of the vector elements representing distinct conformational states of Env. We identify data processing strategies that allow clear separation of the previously characterized closed and open conformations, as well as unliganded and antibody-liganded states of Env when they are present in mixtures. We show that identifying and removing spikes with the lowest signal-to-noise ratios improves the overall accuracy of alignment between individual Env sub-volumes, and that alignment accuracy, in turn, determines the success of image classification in assessing conformational heterogeneity in heterogeneous mixtures. We validate these procedures for computational separation by successfully separating and reconstructing distinct 3D structures for unliganded and antibody-liganded as well as open and closed conformations of Env present simultaneously in mixtures.     

Freezing tolerance and low molecular weight cryoprotectants in an invasive parasitic fly, the deer ked (Lipoptena cervi)

Insect cold hardiness is often mediated by low molecular weight cryoprotectants, such as sugars, polyols, and amino acids (AA). While many free-living northern insects must cope with extended periods of freezing ambient temperatures (Ta), the ectoparasitic deer ked Lipoptena cervi imago can encounter subfreezing Ta only during a short autumnal period between hatching and host location. Subsequently, it benefits from the body temperature of the cervid host for survival in winter. This study investigated the cold tolerance of the species by determining its lower lethal temperature (100% mortality, LLT100) during faster and slower cold acclimation, by determining the supercooling point (SCP) and by measuring the concentrations of potential low molecular weight cryoprotectants. The LLT100 of the deer ked was approximately -16 ° C, which would enable it to survive freezing nighttime Ta not only in its current area of distribution but also further north. The SCP was -7.8 ° C, clearly higher than the LLT100 , indicating that the deer ked displays freezing tolerance. The concentrations of free AA, especially nonessential AA, were higher in the cold-acclimated deer keds similar to several other insects. The concentrations of proline increased together with γ-aminobutyrate, arginine, asparagine, cystine, glutamate, glutamine, hydroxylysine, sarcosine, serine, and taurine. AA could be hypothesized to act as cryoprotectants by, e.g., protecting enzymes and lipid membranes from damage caused by cold.     

Setup and dosimetry for exposure of human skin in vivo to RF-EMF at 900 MHz

The aim of this study was a dosimetrical analysis of an experimental setup used in the exposure of 10 female volunteers to GSM 900 radiation. The exposure was carried out by irradiating a small region of the right forearms of the volunteers for 1 h, after which biopsies were taken from the exposed skin for protein analysis. The source of irradiation was a half-wave dipole fed with a computer controlled GSM phone. The specific absorption rate (SAR) induced in the skin biopsy was assessed by computer simulations. The numerical model of the arm consisted of a muscle tissue simulating cylinder covered with thin skin (1 mm) and fat (3 mm) layers. The simulation models were validated by measurements with a homogeneous cylindrical liquid phantom. The average SAR value in the biopsy was 1.3 W/kg and the estimated uncertainty +/-20% (K = 2). The main source of error was found to be variations in the distance of the forearm from the dipole (10 +/- 1 mm). Other significant sources of uncertainty are individual variations of the fat layer and arm thicknesses, and the uncertainty of radio frequency (RF) power measurement.     

Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues

Our knowledge on tissue- and disease-specific functions of human genes is rather limited and highly context-specific. Here, we have developed a method for the comparison of mRNA expression levels of most human genes across 9,783 Affymetrix gene expression array experiments representing 43 normal human tissue types, 68 cancer types, and 64 other diseases. This database of gene expression patterns in normal human tissues and pathological conditions covers 113 million datapoints and is available from the GeneSapiens website.     

Determinants of reproductive success in voles: space use in relation to food and litter size manipulation

Spacing behaviour of female mammals is suggested to depend on the distribution and abundance of food. In addition, food limitation has been found to constrain the reproductive success of females. However, whether females maximize their reproductive success by adjusting space use in relation to current food availability and reproductive effort (e.g. litter size) has not been experimentally studied. We examined these questions by manipulating simultaneously food resources (control vs. food supplementation) and litter sizes (control vs. plus two pups) of territorial female bank voles (Clethrionomys glareolus) in large outdoor enclosures. Females with supplementary food had smaller home ranges (foraging area) and home range overlaps than control females, whereas litter size manipulation had no effect on space use. In contrast, the size of territory (exclusive area) was not affected by food supplementation or litter size manipulation. As we have previously shown elsewhere, extra food increases the reproductive success of bank vole females in terms of size and proportion of weaned offspring. According to the present data, greater overlap of female home ranges had a negative effect on reproductive success of females, particularly on survival of offspring. We conclude that higher food availability increases the reproductive success of bank vole females, and this effect may be mediated through lower vulnerability of offspring to direct killing and/or detrimental effects from other females in the population. Moreover, it seems that when density of conspecifics is controlled for, home range sizes of females, but not territoriality, is related to food resources in Clethrionomys voles.     

Serum hormone and myocellular protein recovery after intermittent runs at the velocity associated with V˙O2max

The responses of serum myocellular proteins and hormones to exercise were studied in ten well-trained middle-distance runners [maximal oxygen consumption (VO(2max)) = 69.4 (5.1) ml x kg(-1) x min(-1)] during 3 recovery days and compared to various measures of physical performance. The purpose was to establish the duration of recovery from typical intermittent middle-distance running exercises. The subjects performed, in random, order two 28-min treadmill running exercises at a velocity associated with VO(2max): 14 bouts of 60-s runs with 60 s of rest between each run (IR(60)) and 7 bouts of 120-s runs with 120 s of rest between each run (IR(120)). Before the exercises (pre- exercise), 2 h after, and 1, 2 and 3 days after the exercises, the same series of measurements were performed, including those for serum levels of the myocellular proteins creatine kinase, myoglobin and carbonic anhydrase III (S-CK, S-Mb and S-CA III, respectively), serum hormones testosterone, Luteinizing hormone, follicle-stimulating hormone and cortisol (S-testosterone, S-LH, S-FSH and S-cortisol, respectively) and various performance parameters: maximal vertical jump height (CMJ) and stride length, heart rate and ratings of perceived exertion during an 8-min run at 15 km x h(-1) (SL(15 km x h(-1)), HR(15 km x h(-1)) and RPE(15 km x h(-1)), respectively). Two hours after the end of both exercise bouts the concentration of each measured serum protein had increased significantly (P < 0.001) compared to the pre-exercise level, but there were no changes in SL(15 km x h(-1)) or CMJ. During the recovery days only S-CK was significantly raised (P < 0.01), concomitant with a decrease in CMJ (P < 0.01) and an increase in RPE(15 km x h(-1)) (P < 0.01). Hormone levels remained unchanged compared to the pre-exercise levels during the recovery days and there were no significant differences between the two exercise bouts in any of the observed post-exercise day-to-day responses. With the exception of S-CK, after IR(120) the post-exercise responses returned to their pre-exercise levels within the 3 days of recovery. The present findings suggest that a single 28-min intermittent middle-distance running exercise does not induce changes in serum hormones of well-trained runners during recovery over 3 days, while changes in S-CK, CMJ and RPE(15 km x h(-1)) indicate that 2-3 days of light training may be needed before the recovery at muscle level is complete.     

Repeated Home-Applied Dual-Light Antibacterial Photodynamic Therapy Can Reduce Plaque Burden,Inflammation, and aMMP-8 in Peri-Implant Disease—A Pilot Study

Until now, in clinical dentistry, antibacterial photodynamic therapy (aPDT) has been restricted to in-office treatments, which hampers repeated applications. This pilot study tested the benefit of a commercially available Lumoral^® device designed for regular periodontal dual-light aPDT treatment at home. Seven patients with peri-implant disease applied dual-light aPDT daily in addition to their normal dental hygiene for four weeks. A single Lumoral^® treatment includes an indocyanine green mouth rinse followed by 40 J/cm² radiant exposure to a combination of 810 nm and 405 nm light. A point-of-care analysis of active-matrix metalloproteinase (aMMP-8), visible plaque index (VPI), bleeding on probing (BOP), and peri-implant pocket depth (PPD) measurements was performed on day 0, day 15, and day 30. Reductions in aMMP-8 (p = 0.047), VPI (p = 0.03), and BOP (p = 0.03) were observed, and PPD was measured as being 1 mm lower in the implant (p = ns). These results suggest a benefit of regular application of dual-light aPDT in peri-implantitis. Frequently repeated application can be a promising approach to diminishing the microbial burden and to lowering the tissue destructive proteolytic and inflammatory load around dental implants. Further studies in larger populations are warranted to show the long-term benefits.     

Metabolic Engineering of Acinetobacter baylyi ADP1 for Improved Growth on Gluconate and Glucose

A high growth rate in bacterial cultures is usually achieved by optimizing growth conditions, but metabolism of the bacterium limits the maximal growth rate attainable on the carbon source used. This limitation can be circumvented by engineering the metabolism of the bacterium. Acinetobacter baylyi has become a model organism for studies of bacterial metabolism and metabolic engineering due to its wide substrate spectrum and easy-to-engineer genome. It produces naturally storage lipids, such as wax esters, and has a unique gluconate catabolism as it lacks a gene for pyruvate kinase. We engineered the central metabolism of A. baylyi ADP1 more favorable for gluconate catabolism by expressing the pyruvate kinase gene (pykF) of Escherichia coli. This modification increased growth rate when cultivated on gluconate or glucose as a sole carbon source in a batch cultivation. The engineered cells reached stationary phase on these carbon sources approximately twice as fast as control cells carrying an empty plasmid and produced similar amount of biomass. Furthermore, when grown on either gluconate or glucose, pykF expression did not lead to significant accumulation of overflow metabolites and consumption of the substrate remained unaltered. Increased growth rate on glucose was not accompanied with decreased wax ester production, and the pykF-expressing cells accumulated significantly more of these storage lipids with respect to cultivation time.