ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing

Transposon-insertion sequencing (TIS) is a powerful approach for deciphering genetic requirements for bacterial growth in different conditions, as it enables simultaneous genome-wide analysis of the fitness of thousands of mutants. However, current methods for comparative analysis of TIS data do not adjust for stochastic experimental variation between datasets and are limited to interrogation of annotated genomic elements. Here, we present ARTIST, an accessible TIS analysis pipeline for identifying essential regions that are required for growth under optimal conditions as well as conditionally essential loci that participate in survival only under specific conditions. ARTIST uses simulation-based normalization to model and compensate for experimental noise, and thereby enhances the statistical power in conditional TIS analyses. ARTIST also employs a novel adaptation of the hidden Markov model to generate statistically robust, high-resolution, annotation-independent maps of fitness-linked loci across the entire genome. Using ARTIST, we sensitively and comprehensively define Mycobacterium tuberculosis and Vibrio cholerae loci required for host infection while limiting inclusion of false positive loci. ARTIST is applicable to a broad range of organisms and will facilitate TIS-based dissection of pathways required for microbial growth and survival under a multitude of conditions.     

Recent divergences and size decreases of eastern gorilla populations

Compared with other African apes, eastern gorillas (Gorilla beringei) have been little studied genetically. We used analysis of autosomal DNA genotypes obtained from non-invasively collected faecal samples to estimate the evolutionary histories of the two extant mountain gorilla populations and the closely related eastern lowland gorillas. Our results suggest that eastern lowland gorillas and mountain gorillas split beginning some 10 000 years ago, followed 5000 years ago by the split of the two mountain gorilla populations of Bwindi Impenetrable National Park and the Virungas Massif. All three populations have decreased in effective population size, with particularly substantial 10-fold decreases for the mountain gorillas. These dynamics probably reflect responses to habitat changes resulting from climate fluctuations over the past 20 000 years as well as increasing human influence in this densely populated region in the last several thousand years.     

Molecular analysis reveals lowbush blueberry pest predation rates depend on ground beetle (Coleoptera: Carabidae) species and pest density

Molecular gut-content analysis allows determination of pest predation by field-collected predators. Ground beetles (Coleoptera: Carabidae) common in lowbush blueberries may consume blueberry spanworm, Itame argillacearia (Packard) (Lepidoptera: Geometridae), and blueberry flea beetle, Altica sylvia Malloch (Coleoptera: Chrysomelidae), providing pest suppression. Using newly developed pest specific primers, laboratory feeding trials showed that the median detection time (MDT) for blueberry spanworm in the largest beetle, Carabus nemoralis O.F. Müller, was 3.7 h, whereas Poecilus lucublandus (Say) and Pterostichus mutus (Say) had MDTs between 27.1 and 31.6 h for both pests. At a field-site with high pest abundances, the probability of detecting blueberry spanworm and blueberry flea beetle DNA was greater in P. lucublandus, 26 and 39 % respectively, than in P.mutus, 8 and 20 % respectively. Only 0 and 1 % of P. lucublandus and P. mutus, respectively, tested positive for blueberry spanworm DNA at a second site with low abundance. At the first site, the probability of detecting pest DNA in both ground beetle species was positively related to pest density. Higher pest DNA detection rates and captures of ground beetles corresponded to field areas where significant pest reductions occurred from late May to early June. Conservation of predatory carabid beetles could lead to valuable biological control in lowbush blueberries.     

Analysis of stable states in global savannas: is the CART pulling the horse?

Multiple stable states, bifurcations and thresholds are fashionable concepts in the ecological literature, a recognition that complex ecosystems may at times exhibit the interesting dynamic behaviours predicted by relatively simple biomathematical models. Recently, several papers in Global Ecology and Biogeography, Proceedings of the National Academy of Sciences USA, Science and elsewhere have attempted to quantify the prevalence of alternate stable states in the savannas of Africa, Australia and South America, and the tundra–taiga–grassland transitions of the circum‐boreal region using satellite‐derived woody canopy cover. While we agree with the logic that basins of attraction can be inferred from the relative frequencies of ecosystem states observed in space and time, we caution that the statistical methodologies underlying the satellite product used in these studies may confound our ability to infer the presence of multiple stable states. We demonstrate this point using a uniformly distributed ‘pseudo‐tree cover’ database for Africa that we use to retrace the steps involved in creation of the satellite tree‐cover product and subsequent analysis. We show how classification and regression tree (CART)‐based products may impose discontinuities in satellite tree‐cover estimates even when such discontinuities are not present in reality. As regional and global remote sensing and geospatial data become more easily accessible for ecological studies, we recommend careful consideration of how error distributions in remote sensing products may interact with the data needs and theoretical expectations of the ecological process under study.     

Glass Delamination: a Comparison of the Inner Surface Performance of Vials and Pre-filled Syringes

The occurrence of glass delamination is a serious concern for parenteral drug products. Over the past several years, there has been a series of product recalls involving glass delamination in parenteral drugs stored in vials which has led to heightened industry and regulatory scrutiny. In this study, a two-pronged approach was employed to assess the inner surface durability of vials and pre-filled syringes. Non-siliconized syringes were used in order to directly compare glass to glass performance between vials and syringes. The vial and syringe performance was screened with pharmaceutically relevant formulation conditions. The influence of pH, buffer type, ionic strength, and glass type and source was evaluated. In addition, an aggressive but discriminating formulation condition (glutaric acid, pH 11) was used to ascertain the impact of syringe processing. Advanced analytical tools including inductively coupled plasma/mass spectrometry, scanning electron microscopy, atomic force microscopy, and dynamic secondary ion mass spectroscopy showed significant differences in glass performance between vials and syringes. Pre-filled syringes outperform vials for most tests and conditions. The manufacturing conditions for vials lead to glass defects, not found in pre-filled syringes, which result in a less chemically resistant surface. The screening methodology presented in this work can be applied to assess suitability of primary containers for specific drug applications.Key words: borosilicate vials, glass delamination, glass corrosion, hydrolytic resistance, pre-filled syringes     

A Simple,Quantitative Method Using Alginate Gel to Determine Rat Colonic Tumor Volume In Vivo

Many studies of the response of colonic tumors to therapeutics use tumor multiplicity as the endpoint to determine the effectiveness of the agent. These studies can be greatly enhanced by accurate measurements of tumor volume. Here we present a quantitative method to easily and accurately determine colonic tumor volume. This approach uses a biocompatible alginate to create a negative mold of a tumor-bearing colon; this mold is then used to make positive casts of dental stone that replicate the shape of each original tumor. The weight of the dental stone cast correlates highly with the weight of the dissected tumors. After refinement of the technique, overall error in tumor volume was 16.9% ± 7.9% and includes error from both the alginate and dental stone procedures. Because this technique is limited to molding of tumors in the colon, we utilized the Apc^Pirc/+ rat, which has a propensity for developing colonic tumors that reflect the location of the majority of human intestinal tumors. We have successfully used the described method to determine tumor volumes ranging from 4 to 196 mm³. Alginate molding combined with dental stone casting is a facile method for determining tumor volume in vivo without costly equipment or knowledge of analytic software. This broadly accessible method creates the opportunity to objectively study colonic tumors over time in living animals in conjunction with other experiments and without transferring animals from the facility where they are maintained.Colon cancer is the third leading cause of cancer in men and women, with more than 100,000 new cases diagnosed each year in the United States alone. This disease is not limited to humans—cancers of the colon and rectum also affect companion species, such as dogs, albeit less frequently than in humans.²⁰ Colorectal cancers generally develop from precancerous polyps, which can be detected and removed during colonoscopy screening before they become invasive cancers. However, not all precancers will become cancerous,²³ and a better understanding of early tumor growth dynamics in models of the disease can simultaneously increase the rate of detection of polyps destined to become cancerous and decrease the rate of unnecessary removal of benign polyps.Sizing of tumors creates an additional dimension beyond studies examining tumor multiplicity alone. Terminal sizing of tumors uses an eyepiece reticule under a dissection microscope to measure the maximal diameter of each tumor. However, this method likely misrepresents tumor volume for several reasons. First, tumors often are not symmetrical in shape, thereby limiting the interpretation of even multiple linear measurements. When volume calculations rely on the use of a formula, the irregular shape of solid tumors may require the testing of many different formulas to find the optimal one for that particular measurement and model.⁸ Second, if tumor sizing occurs after fixation, the original shape of the tumor can be affected. However, when tumor sizing occurs before fixation, the added time to size the tumors may result in degradation of the intestinal tissue, limiting further analysis. An alternate method of tumor sizing involves using the surrogate of tumor weight, the current ‘gold standard,’ for terminal studies. Tumor weight correlates closely with tumor size, although tumor density may vary depending on the tumor type. In addition, this technique is limited to use at the terminal time point. Methods that determine true tumor volume are powerful; those that can be applied in vivo to study the tumor longitudinally are even more compelling.It recently has been recognized that not all early colonic tumors grow; some remain static for years whereas a few spontaneously regress.²³ Importantly, the early growth profile of a tumor may correlate with its eventual fate.²³ This aspect of tumor biology is a newly emerging area that deserves deeper study. The current gold standard for determining longitudinal tumor volume is CT, given that tumor weight is available only through terminal experiments. In mice, microCT colonography can be used to detect a 16% change in tumor volume with 95% confidence in living animals.⁵ However, the cost of CT equipment limits this technology to shared facilities, and the pathogen status of these facilities may preclude returning animals to the place where they were original housed, limiting the opportunities for longitudinal study. Importantly, many institutions do not have access to microCT technology, and even if available, 3D renderings must be recreated to determine tumor volume, a process requiring specialized software and detailed computing knowledge. Furthermore, CT exposes animal subjects to radiation, which may interfere with the tumor biology. Although MRI can be used to determine tumor volume accurately in the absence of ionizing radiation, specialized scanners and software are required, and enemas or intravenous treatments are needed to visualize tumors clearly.²⁶Another imaging modality uses the surface area of signal due to proteins expressing a fluorescent marker, such as red fluorescent protein, as a surrogate for tumor volume.¹⁷ However, tumor volume measured by fluorescent surface area¹² may not accurately represent tumor volume in irregularly shaped tumors. In addition, this method necessitates a surgical procedure to orthotopically transplant fluorophore-expressing cells, raising questions of immune interactions between the recipient animal and the donor cells or to the surgery itself. If nude or immunocompromised animals are used in the procedure, the ability to study the immune aspect of tumor biology is reduced or eliminated.Alternatively, tumor volume can be estimated from endoscopic images. The study of tumors by colonoscopy has become routine for both mouse^6,10 and rat^1,15 models of the disease. In contrast to terminal assessments, colonoscopy allows tumors to be visualized in vivo over time, capturing the dynamics of tumor growth. Documentation of this aspect of tumor biology can greatly enrich studies evaluating chemopreventive or therapeutic agents.^6,15 Quantitative methods for determining tumor volume take this benefit a step further, allowing the investigation of the effects of background strain, therapeutic agents, environmental factors, or other modifiers of tumor growth pattern. One method to estimate tumor size uses the fraction of luminal cross-section occluded by tumor.² However, the colonic lumen expands as the animal grows, and its size often increases to accommodate the growing tumor, to prevent intestinal blockage. Optical methods to extrapolate tumor sizes from 2D images obtained in vivo during colonoscopy are achieved by inserting a flexible metal rod of known dimensions into the working channel of the endoscope.¹⁰ However, because colonic tumors can differ in shape (some are flat whereas others are pedunculated), area measurements may not translate accurately to tumor volume.To overcome these limitations and to add another tool to the growing cancer-research toolbox, we have developed a method using a biologically inert alginate to create negative molds of colonic tumors. These molds are filled with dental stone to achieve a positive cast of each tumor. A conversion factor then is used to calculate the volume of the original tumor from the dry weight of the dental stone cast. This procedure, which requires no specialized or expensive equipment and no complicated analytical methods, can be performed within the facility where the rats are housed and takes less than 15 min, including the 8 to 12 min during which the alginate sets. Therefore, our new method offers possibilities to study the dynamics of tumor growth in virtually any animal facility, regardless of the health status of subject animals or equipment availability.     

Combined Impact of Cardiorespiratory Fitness and Visceral Adiposity on Metabolic Syndrome in Overweight and Obese Adults in Korea

Background

Obesity, especially visceral obesity, is known to be an important correlate for cardiovascular disease and increased mortality. On the other hand, high cardiorespiratory fitness is suggested to be an effective contributor for reducing this risk. This study was conducted to determine the combined impact of cardiorespiratory fitness and visceral adiposity, otherwise known as fitness and fatness, on metabolic syndrome in overweight and obese adults.

Methods

A total of 232 overweight and obese individuals were grouped into four subtypes according to their fitness level. This was measured by recovery heart rate from a step test in addition to visceral adiposity defined as the visceral adipose tissue area to subcutaneous adipose tissue area ratio (VAT/SAT ratio). Associations of fitness and visceral fatness were analyzed in comparison with the prevalence of metabolic syndrome.

Results

The high visceral fat and low fitness group had the highest prevalence of metabolic syndrome [Odds Ratio (OR) 5.02; 95% Confidence Interval (CI) 1.85–13.61] compared with the reference group, which was the low visceral adiposity and high fitness group, after adjustments for confounding factors. Viscerally lean but unfit subjects were associated with a higher prevalence of metabolic syndrome than more viscerally obese but fit subjects (OR 3.42; 95% CI 1.27–9.19, and OR 2.70; 95% CI 1.01–7.25, respectively).

Conclusions

Our study shows that visceral obesity and fitness levels are cumulatively associated with a higher prevalence of metabolic syndrome in healthy overweight and obese adults. This suggests that cardiorespiratory fitness is a significant modifier in the relation of visceral adiposity to adverse metabolic outcomes in overweight and obese individuals.