The model organism as a system: integrating 'omics' data sets

Various technologies can be used to produce genome-scale, or 'omics', data sets that provide systems-level measurements for virtually all types of cellular components in a model organism. These data yield unprecedented views of the cellular inner workings. However, this abundance of information also presents many hurdles, the main one being the extraction of discernable biological meaning from multiple omics data sets. Nevertheless, researchers are rising to the challenge by using omics data integration to address fundamental biological questions that would increase our understanding of systems as a whole.     

Expression of Fibroblast Growth Factor-21 in Muscle Is Associated with Lipodystrophy,Insulin Resistance and Lipid Disturbances in Patients with HIV

BackgroundFibroblast growth factor (FGF)-21 is a novel regulator of glucose and lipid metabolism. Recently, increased FGF-21 mRNA expression in muscle was found in patients with type 2 diabetes, but the role for FGF-21 in muscle is not well understood. Patients with HIV-infection and lipodystrophy are characterised by various degree of lipid-driven insulin resistance. We hypothesized that muscle FGF-21 mRNA would be altered in HIV patients with lipodystrophy.DesignTwenty-five HIV-infected men with lipodystrophy (LD) and 15 age-matched healthy controls, received an oral glucose tolerance test and a euglycemic-hyperinsulinemic clamp (50 mU/m2/min) combined with 6,6-H₂ glucose infusion. Muscle biopsies were obtained and FGF-21 mRNA and glycogen synthase (GS) activity were measured.ResultsSubjects with HIV were insulin resistant compared with non-HIV subjects. Compared to controls, HIV subjects demonstrated a twofold increase of plasma FGF-21 from 70.4±56.8 pg/ml vs 109.1±71.8 pg/ml, respectively (p = 0.04) and an eight-fold increase in muscular FGF-21 mRNA expression (p = 0.001). Muscle FGF-21 mRNA correlated inversely with the rate of disappearance of glucose during insulin clamp (r = −0.54, p = 0.0009), and the GS fractional velocity in muscle (r = −0.39, p = 0.03), and directly with fasting insulin (r = 0.50, p = 0.0022), HOMA-IR (r = 0.47, p = 0.004), triglycerides (r = 0.60. P = 0.0001), waist-to-hip ratio (r = 0.51, p = 0.0001) and limb fat mass (−0.46, p = 0.004), but not to plasma FGF-21.ConclusionFGF-21 mRNA is increased in skeletal muscle in HIV patients and correlates to whole-body (primarily reflecting muscle) insulin resistance, but not to plasma FGF-21. Those findings add to the evidence that FGF-21 is a myokine and may suggest that muscle FGF-21 is working in a local manner.     

Betaine will protect hybridoma cells from hyperosmotic stress

Summary Hyperosmolality adversely affects growth of murine hybridoma cells. Addition of low concentrations of betaine to the growth medium will protect the hyperosmotically stressed cells. The protective effect is observed as increased growth rate and cell density of the stressed cell cultures. The cellular production of monoclonal antibody is related to growth rate in an inverse fashion.     

Sexual Functioning and Obesity: A Review

We review the literature on the relationship between obesity and sexual functioning. Eleven population‐based studies, 20 cross‐sectional non‐population‐based studies, and 16 weight loss studies are reviewed. The consistency of findings suggests that the relationship between obesity and reduced sexual functioning is robust, despite diverse methods, instruments, and settings. In most population‐based studies, erectile dysfunction (ED) is more common among obese men than among men of recommended weight. Studies of patients in clinical settings often include individuals with higher degrees of obesity, with most studies showing a relationship between obesity and lower levels of sexual functioning, especially ED. The few studies that include both genders generally report more problems among women. Most studies of patients with comorbidities associated with obesity also find an association between obesity and reduced sexual functioning. Most weight loss studies demonstrate improvement in sexual functioning concurrent with weight reduction despite varying study designs, weight loss methods, and follow‐up periods. We recommend that future studies (i) investigate differences and similarities between men and women with respect to obesity and sexual functioning, (ii) use instruments that go beyond the assessment of sexual dysfunction to include additional concepts such as sexual satisfaction, interest, and arousal and, (iii) assess how and the degree to which obese individuals are affected by sexual difficulties. Given the high prevalence of obesity and the inverse association between body mass and sexual functioning, we also recommend that sexual functioning should be more fully addressed by clinicians, both in general practice and in weight loss programs.     

Up,up, and away: relative importance of horizontal and vertical escape from predators for survival and senescence

Animals fleeing a potential predator can escape horizontally or vertically, although vertical flight is more expensive than horizontal flight. The ability to escape in three dimensions by flying animals has been hypothesized to result in greater survival and eventually slower senescence than in animals only fleeing in two dimensions. In a comparative study of flight initiation distance in 69 species of birds when approached by a human, I found that the amount of variance explained by flight initiation distance was more than four times as large for the horizontal than the vertical component of perch height when taking flight. The slope of the relationship between horizontal distance and flight initiation distance (horizontal slope) increased with increasing body mass across species, whereas the slope of the relationship between vertical distance and flight initiation distance (vertical slope) decreased with increasing body mass. Therefore, there was a negative relationship between horizontal and vertical slope, although this negative relationship was significantly less steep than expected for a perfect trade‐off. The horizontal slope decreased with increasing density of the habitat from grassland over shrub to forest, whereas that was not the case for the vertical slope. Adult survival rate increased and rate of senescence (longevity adjusted for survival rate, body mass and sampling effort) decreased with increasing vertical, but not with horizontal slope, consistent with the prediction that vertical escape indeed provides a means of reducing the impact of predation.     

Barnacle Settlement on Hydrogels

Settlement of cultured Balanus amphitrite cyprid larvae was tested on different non-solid hydrogel surfaces. Gels consisting of alginate (highly anionic), chitosan (highly cationic), polyvinyl alcohol substituted with light-sensitive stilbazolium groups (PVA-SbQ; very low cationic) and agarose (neutral) were applied in cell culture multi-well plates. Polystyrene served as a solid surface reference. Preliminary experiments were performed to determine whether any substances leaching out of the gels could inhibit barnacle settlement. Whilst leachate from the gels revealed no toxicity towards Artemia salina nauplius larvae, PVA-SbQ in solution at and above a concentration of 0.4 ppm inhibited B. amphitrite cyprid settlement. Gels were therefore washed to avoid such effects during further testing, and toxicity and settlement tests with B. amphitrite nauplii and cyprids, respectively, applied to verify that washing was effective. Settlement was tested directly on the different test materials, followed by a quality test of non-settled larvae. All gels inhibited barnacle settlement compared to the polystyrene controls. Gels consisting of 2.5% PVA-SbQ or 0.5% agarose showed promising antifouling properties. Although some settlement occurred on 2.5% PVA-SbQ gels, metamorphosis was clearly inhibited. Only 10% of the larvae had settled on 0.5% agarose gels after 8 d. Less than 40% settlement occurred on alginate gels, as well as on 2% chitosan gels. Quality testing showed that the majority of remaining non-settled larvae in all gel experiments were able to settle when offered a suitable solid substratum.     

A method for determination of fresh weight of aquatic organisms

A precise and rapid method is described for the determination of fresh weight of aquatic plants and animals. The determination of fresh weight is done gravimetrically with a spectrophotometric estimate of adherent water providing a correction for adherent water.     

Isolation and characterisation of dog uropathogenic Escherichia coli strains and their fimbriae

A number of Escherichia coli strains have been isolated from dogs with urinary tract infections. These strains have been characterised with respect to their O, K, H, and fimbrial antigens, colicin production, antibiotic resistance, plasmid content and their ability to haemagglutinate erythrocytes from various species. Crossed immunoelectrophoresis of fimbrial extracts, as well as the reaction of partly purified fimbriae of a number of these strains with monoclonal antibodies revealed homology or a strong crossereaction with an F12 fimbrial subunit protein of human uropathogenic E. coli strains. Unlike human F12 fimbriae producing strains, the dog isolates did agglutinate dog erythrocytes in the presence of D-mannose but not human erythrocytes, indicating that the adhesin carried by these strains is different from the adhesin on fimbriae of human uropathogenic E. coli. Similar indications were obtained from experiments with latex beads coated with the receptor for P-fimbriae. These beads were agglutinated by Escherichia coli strains from human urinary tract infections, but not by the dog isolates described here. Preliminary adhesion experiments of human and dog Escherichia coli to human bladder epithelial and canine kidney epithelial cells also showed differences in adhesion depending on the origin of the strain tested.