Computer simulations improve university instructional laboratories

Laboratory classes are commonplace and essential in biology departments but can sometimes be cumbersome, unreliable, and a drain on time and resources. As university intakes increase, pressure on budgets and staff time can often lead to reduction in practical class provision. Frequently, the ability to use laboratory equipment, mix solutions, and manipulate test animals are essential learning outcomes, and "wet" laboratory classes are thus appropriate. In others, however, interpretation and manipulation of the data are the primary learning outcomes, and here, computer-based simulations can provide a cheaper, easier, and less time- and labor-intensive alternative. We report the evaluation of two computer-based simulations of practical exercises: the first in chromosome analysis, the second in bioinformatics. Simulations can provide significant time savings to students (by a factor of four in our first case study) without affecting learning, as measured by performance in assessment. Moreover, under certain circumstances, performance can be improved by the use of simulations (by 7% in our second case study). We concluded that the introduction of these simulations can significantly enhance student learning where consideration of the learning outcomes indicates that it might be appropriate. In addition, they can offer significant benefits to teaching staff.     

The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions

We have determined the structure to 2.8 A of an RNA aptamer (F5), containing 2'-deoxy-2-aminopurine (2AP) at the -10 position, complexed with MS2 coat protein by soaking the RNA into precrystallised MS2 capsids. The -10 position of the RNA is an important determinant of binding affinity for coat protein. Adenine at this position in other RNA stem-loops makes three hydrogen bonds to protein functional groups. Substituting 2AP for the -10 adenine in the F5 aptamer yields an RNA with the highest yet reported affinity for coat protein. The refined X-ray structure shows that the 2AP base makes an additional hydrogen bond to the protein compared to adenine that is presumably the principal origin of the increased affinity. There are also slight changes in phosphate backbone positions compared to unmodified F5 that probably also contribute to affinity. Such phosphate movements are common in structures of RNAs bound to the MS2 T = 3 protein shell and highlight problems for de novo design of RNA binding ligands.     

Reversible dissociation of the plant golgi apparatus by brefeldin A

Summary— The effects of the drug Brefeldin A, shown to block the translocation of proteins between the endoplasmic reticulum and the Golgi apparatus in animal cells, were studied on different plant cell systems. In suspension culture cells and root tissues, the Golgi aparatus was affected by Brefeldin A treatments resulting in distortion and dissociation of the Golgi stacks, coupled with appearance of numerous vesicles in the cytoplasm. This process was reversible. Therefore, Brefeldin A provides a powerful tool with which to study Golgi dynamics and function in plant as well as in animal cells.     

Development of Health‐Related Waist Circumference Thresholds Within BMI Categories

Objective: To develop and cross‐validate waist circumference (WC) thresholds within BMI categories. The utility of the derived values was compared with the single WC thresholds (women, 88 cm; men, 102 cm) recommended by NIH and Health Canada. Research Methods and Procedures: The sample included adults classified as normal weight (BMI = 18.5 to 24.9), overweight (BMI = 25 to 29.9), obese I (BMI = 30 to 34.9), and obese II+ (BMI ≥ 35) from the Third U.S. National Health and Nutrition Examination Survey (NHANES III; n = 11, 968) and the Canadian Heart Health Surveys (CHHS; n = 6286). Receiver operating characteristic curves were used to determine the optimal WC thresholds that predicted high risk of coronary events (top quintile of Framingham scores) within BMI categories using the NHANES III. The BMI‐specific WC thresholds were cross‐validated using the CHHS. Results: The optimal WC thresholds increased across BMI categories from 87 to 124 cm in men and from 79 to 115 cm in women. The validation study indicated improved sensitivity and specificity with the BMI‐specific WC thresholds compared with the single thresholds. Discussion: Compared with the recommended WC thresholds, the BMI‐specific values improved the identification of health risk. In normal weight, overweight, obese I, and obese II+ patients, WC cut‐offs of 90, 100, 110, and 125 cm in men and 80, 90, 105, and 115 cm in women, respectively, can be used to identify those at increased risk.     

Indirect competitive immunoassay for detection of aflatoxin B1 in corn and nut products using the array biosensor

Because of the potential health risks of aflatoxin B₁ (AFB₁), it is essential to monitor the level of this mycotoxin in a variety of foods. An indirect competitive immunoassay has been developed using the NRL array biosensor, offering rapid, sensitive detection and quantification of AFB₁ in buffer, corn and nut products. AFB₁-spiked foods were extracted with methanol and Cy5-anti-AFB₁ added to the resulting sample. The extracted sample/antibody mix was passed over a waveguide surface patterned with immobilized AFB₁. The resulting fluorescence signal decreased as the concentration of AFB₁ in the sample increased. The limit of detection for AFB₁ in buffer, 0.3 ng/ml, was found to increase to between 1.5 and 5.1 ng/g and 0.6 and 1.4 ng/g when measured in various corn and nut products, respectively.     

HIV incidence, risk factors, and motivation for biomedical intervention among gay, bisexual men, and transgender persons in Northern Thailand

Background

HIV prevalence among men who have sex with men (MSM) and transgender (TG) persons is high and increasing in Chiang Mai, northern Thailand.

Objectives

To describe demographic, socioeconomic, sexual behavior and interest in future HIV prevention trials among gay and bisexual MSM and TG presenting for HIV testing (VCT) and pre-screening for the iPrEx pre-exposure chemoprophylaxis trail.

Methods

In 2008–09, MSM/TG participants attending VCT were interviewed and tested for HIV and STI. Univariate and multivariate regression analyses were done to assess associations with HIV infection.

Results

A total of 551 MSM clients (56.1% gay, 25.4% TG, and 18.5% bisexual (BS)) were enrolled. The mean age was 23.9 years. HIV prevalence among MSM overall was 12.9% (71/551); 16.5% among gay men, 9.3% among TG, and 6.9% among BS. Consistent use of condom was low, 33.3% in insertive anal sex and 31.9% in receptive anal sex. Interest in participation was high, 86.3% for PrEP, 69.7% for HIV vaccine trials, but 29.9% for circumcision. HIV was independently associated with being gay identified, aOR 2.8, p = 0.037 and with being aged 25–29, aOR 2.7, p = 0.027. Among repeat testers, HIV incidence was 8.2/100 PY, 95% CI, 3.7/100PY to 18.3/100PY.

Conclusion

HIV risks and rates varied by self-reported sexual orientation and gender identity. HIV was associated with sexual practices, age, and being gay-identified. These are populations are in need of novel prevention strategies and willing to participate in prevention research.     

The spatial origin of a perceptual transition in binocular rivalry

When the left and the right eye are simultaneously presented with incompatible images at overlapping retinal locations, an observer typically reports perceiving only one of the two images at a time. This phenomenon is called binocular rivalry. Perception during binocular rivalry is not stable; one of the images is perceptually dominant for a certain duration (typically in the order of a few seconds) after which perception switches towards the other image. This alternation between perceptual dominance and suppression will continue for as long the images are presented. A characteristic of binocular rivalry is that a perceptual transition from one image to the other generally occurs in a gradual manner: the image that was temporarily suppressed will regain perceptual dominance at isolated locations within the perceived image, after which its visibility spreads throughout the whole image. These gradual transitions from perceptual suppression to perceptual dominance have been labeled as traveling waves of perceptual dominance. In this study we investigate whether stimulus parameters affect the location at which a traveling wave starts. We varied the contrast, spatial frequency or motion speed in one of the rivaling images, while keeping the same parameter constant in the other image. We used a flash-suppression paradigm to force one of the rival images into perceptual suppression. Observers waited until the suppressed image became perceptually dominant again, and indicated the position at which this breakthrough from suppression occurred. Our results show that the starting point of a traveling wave during binocular rivalry is highly dependent on local stimulus parameters. More specifically, a traveling wave most likely started at the location where the contrast of the suppressed image was higher than that of the dominant one, the spatial frequency of the suppressed image was lower than that of the dominant one, and the motion speed of the suppressed image was higher than that of the dominant one. We suggest that a breakthrough from suppression to dominance occurs at the location where salience (the degree to which a stimulus element stands out relative to neighboring elements) of the suppressed image is higher than that of the dominant one. Our results further show that stimulus parameters affecting the temporal dynamics during continuous viewing of rival images described in other studies, also affect the spatial origin of traveling waves during binocular rivalry.     

LRGUK-1 Is Required for Basal Body and Manchette Function during Spermatogenesis and Male Fertility

Male infertility affects at least 5% of reproductive age males. The most common pathology is a complex presentation of decreased sperm output and abnormal sperm shape and motility referred to as oligoasthenoteratospermia (OAT). For the majority of OAT men a precise diagnosis cannot be provided. Here we demonstrate that leucine-rich repeats and guanylate kinase-domain containing isoform 1 (LRGUK-1) is required for multiple aspects of sperm assembly, including acrosome attachment, sperm head shaping and the initiation of the axoneme growth to form the core of the sperm tail. Specifically, LRGUK-1 is required for basal body attachment to the plasma membrane, the appropriate formation of the sub-distal appendages, the extension of axoneme microtubules and for microtubule movement and organisation within the manchette. Manchette dysfunction leads to abnormal sperm head shaping. Several of these functions may be achieved in association with the LRGUK-1 binding partner HOOK2. Collectively, these data establish LRGUK-1 as a major determinant of microtubule structure within the male germ line.     

The work of the Animal Research Station, Cambridge

This paper traces the history of the Animal Research Station, Cambridge from its establishment in 1932 to its closure in 1986. The author worked there for forty years and was Director from 1979. Originally set up as a field station for Cambridge University's School of Agriculture, the Station was expanded after World War II as the Agricultural Research Council's Unit of Animal Reproduction. Beginning with semen and artificial insemination, research at the Station soon embraced superovulation and embryo transfer in farm animals. Many other technologies were also developed here, including IVF in pigs, cloning by nuclear transplantation of early embryonic cells, and the first genetically modified farm animals in Britain. This account recalls the Directors of the Station and their research teams together with details of their pioneering contribution to reproductive biology.