A New Hand‐Held Indirect Calorimeter to Measure Postprandial Energy Expenditure

Objective: To verify the accuracy of a new hand‐held metabolic rate measuring device (MedGem) in quantifying postprandial energy expenditure (PP EE). MedGem measurements were compared to measurements obtained with a conventional indirect calorimeter (Delta‐Trac). Research Methods and Procedures: The resting metabolic rate of 15 healthy subjects was measured for 20 minutes using Delta‐Trac followed by a 10‐minute measurement period using MedGem. EE was again measured for 7 hours after consumption of a 2510‐kJ breakfast. Measurements were read from the Delta‐Trac for the initial 50 minutes of each hour followed by a single reading from the MedGem after 5 to 10 minutes of measurement. Measured EE was calculated as the average of the total measurement period for Delta‐Trac and for eight readings using MedGem; PP EE was calculated as the average of all measurements obtained after breakfast consumption. Results: There was no difference in resting metabolic rate between the two methods (6455.1 ± 417.6 vs. 6468.5 ± 337.2 kJ/d for Delta‐Trac and MedGem, respectively). Measured EE and PP EE values with Delta‐Trac (7019.1 ± 400.8 and 7099.8 ± 399.2 kJ/d, respectively) and MedGem (6775.6 ± 372.0 and 6819.5 ± 379.9 kJ/d, respectively) were not significantly different. There was no bias detected in any of the measurements made with MedGem compared with those of Delta‐Trac. Discussion: The new hand‐held EE measuring device can accurately track PP EE relative to a conventional indirect calorimetry system and, therefore, provides a new opportunity to assess PP EE in research settings and large‐scale trials.     

Response of female beetles to LIDAR derived topographic variables in Eastern boreal mixedwood forests (Coleoptera, Carabidae)

Biodiversity monitoring is increasingly being bolstered with high resolution data derived from remote sensing such as LIDAR (Light Detection and Ranging). We derived a series of topographical variables, including slope, azimuth, ground curvature and flow accumulation from LIDAR images and compared these to captures of female carabids in pitfall traps in Eastern boreal mixedwood forests. We developed a series of species-specific logistic models predicting the proportion of females for eight dominant species, including Agonum retractum, Calathus ingratus, Platynus decentis, Pterostichus adstrictus, Pterostichus coracinus, Pterostichus pensylvanicus, Sphaeroderus nitidicollis and Synuchus impunctatus. We used these models to test three hypotheses related to how the modest topography in boreal forests could influence the availability of microhabitats and possibly potential sites for oviposition and larval development. In general, topographic features such as north facing slopes and high flow accumulation were important predictors of the proportion of females. Models derived from larger scale topography, such as hillsides or small watersheds on the order of ¼-1 ha were better predictors of the proportion of females than were models derived from finer scale topography such as hummocks and small depressions. We conclude that topography likely influences the distribution of carabids based on hydrological mechanisms rather than factors related to temperature. We further suggest based on the scale of responses that these hydrological mechanisms may be linked to the attenuation of past disturbances by wildfire and the propensity of unburned forest patches and fire skips.     

Obesity‐related hypertension: Pathogenesis,cardiovascular risk,and treatment—A position paper of the The Obesity Society and the American Society of Hypertension

In light of the worldwide epidemic of obesity, and in recognition of hypertension as a major factor in the cardiovascular morbidity and mortality associated with obesity, The Obesity Society and The American Society of Hypertension agreed to jointly sponsor a position paper on obesity‐related hypertension to be published jointly in the journals of each society. The purpose is to inform the members of both societies, as well as practicing clinicians, with a timely review of the association between obesity and high blood pressure, the risk that this association entails, and the options for rational, evidenced‐based treatment. The position paper is divided into six sections plus a summary as follows: pathophysiology, epidemiology and cardiovascular risk, the metabolic syndrome, lifestyle management in prevention and treatment, pharmacologic treatment of hypertension in the obese, and the medical and surgical treatment of obesity in obese hypertensive patients. Obesity (2012)     

Multiplex Identification of Microbes

We have adapted molecular inversion probe technology to identify microbes in a highly multiplexed procedure. This procedure does not require growth of the microbes. Rather, the technology employs DNA homology twice: once for the molecular probe to hybridize to its homologous DNA and again for the 20-mer oligonucleotide barcode on the molecular probe to hybridize to a commercially available molecular barcode array. As proof of concept, we have designed, tested, and employed 192 molecular probes for 40 microbes. While these particular molecular probes are aimed at our interest in the microbes in the human vagina, this molecular probe method could be employed to identify the microbes in any ecological niche.The substantial majority of the earth''s bacteria have not been grown in culture and do not form colonies on agar plates (for examples, see references 19 and 21). These statements are particularly true of the bacteria living in or on human beings (for examples, see references 2, 6, and 7). The Human Microbiome Project (for examples, see references 2, 5, 24, and 27) is employing DNA sequencing and other genome-based technologies to reveal the plethora of microbes living in or on humans. Our goal was to develop a massively multiplex method employing currently commercially available reagents to identify those microbes at the species level.Several useful approaches to the identification of microbes that do not form colonies on agar plates have been published. Many scientists have employed dideoxy sequencing of the PCR-amplified 16S rRNA gene to identify microbes (for an example, see reference 22). Dideoxy sequencing is expensive, cumbersome, and slow. “Next-generation” sequencing reduces the cost of sequencing but produces much shorter read lengths. As examples, Tarnberg et al. (26), Jonasson et al. (11), and Sundquist et al. (25) employed pyrosequencing of small portions of the 16S rRNA gene to identify microbes. These scientists could not always identify the microbes down to the species level. “Checkerboard DNA-DNA hybridization” (CDH) is a technology that is more than a decade old (23). Nikolaitchouk et al. (14) have applied CDH to identify the microbes in the human female genital tract and achieved a 13-plex reaction. Dumonceaux et al. (4) coupled microbe-specific oligonucleotides to fluorescently labeled microspheres. Subsequently, the microbes were detected and counted by flow cytometry. Dumonceaux et al. (4) achieved a 9-plex reaction. DeSantis et al. (3) designed and employed a microarray containing 297,851 oligonucleotide probes derived from the 16S rRNA gene from 842 subfamilies of prokaryotes. DeSantis et al. (3) concluded that their microarray revealed greater prokaryotic diversity than dideoxy sequencing of a “typically sized clone library.”None of these ingenious methods meets the requirements for a robust, commercially available, highly multiplex technology. Therefore, we have adapted an independent method to identify microbes: molecular inversion probes (8) coupled with a commercial molecular barcode array. This method does not require growth of the microbes. Rather, molecular probe technology is a nucleic acid-based technology employing DNA homology twice: once for the molecular probe to hybridize to its homologous DNA and again for the 20-mer oligonucleotide barcode on the molecular probe to hybridize to a commercially available oligonucleotide barcode array. We present here data demonstrating proof of concept in which molecular probes were designed, tested, and employed to detect microbes in simulated clinical samples. Because of our ongoing interest in the bacteria that inhabit the adult human vagina (10), we focus on that ecological niche. However, this method is sufficiently general that it can be applied to detect the microbes in any ecological niche, e.g., soil and the ocean.     

Medium‐Chain Triglycerides Increase Energy Expenditure and Decrease Adiposity in Overweight Men

Objective: The objectives of this study were to compare the effects of diets rich in medium‐chain triglycerides (MCTs) or long‐chain triglycerides (LCTs) on body composition, energy expenditure, substrate oxidation, subjective appetite, and ad libitum energy intake in overweight men. Research Methods and Procedures: Twenty‐four healthy, overweight men with body mass indexes between 25 and 31 kg/m² consumed diets rich in MCT or LCT for 28 days each in a crossover randomized controlled trial. At baseline and after 4 weeks of each dietary intervention, energy expenditure was measured using indirect calorimetry, and body composition was analyzed using magnetic resonance imaging. Results: Upper body adipose tissue (AT) decreased to a greater extent (p < 0.05) with functional oil (FctO) compared with olive oil (OL) consumption (?0.67 ± 0.26 kg and ?0.02 ± 0.19 kg, respectively). There was a trend toward greater loss of whole‐body subcutaneous AT volume (p = 0.087) with FctO compared with OL consumption. Average energy expenditure was 0.04 ± 0.02 kcal/min greater (p < 0.05) on day 2 and 0.03 ± 0.02 kcal/min (not significant) on day 28 with FctO compared with OL consumption. Similarly, average fat oxidation was greater (p = 0.052) with FctO compared with OL intake on day 2 but not day 28. Discussion: Consumption of a diet rich in MCTs results in greater loss of AT compared with LCTs, perhaps due to increased energy expenditure and fat oxidation observed with MCT intake. Thus, MCTs may be considered as agents that aid in the prevention of obesity or potentially stimulate weight loss.     

A method for high‐throughput production of sequence‐verified DNA libraries and strain collections

The low costs of array‐synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. However, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost‐effective method called Recombinase Directed Indexing (REDI), which involves integration of a complex library into yeast, site‐specific recombination to index library DNA, and next‐generation sequencing to identify desired clones. We used REDI to generate a library of ~3,300 DNA probes that exhibited > 96% purity and remarkable uniformity (> 95% of probes within twofold of the median abundance). Additionally, we created a collection of ~9,000 individually accessible CRISPR interference yeast strains for > 99% of genes required for either fermentative or respiratory growth, demonstrating the utility of REDI for rapid and cost‐effective creation of strain collections from oligonucleotide pools. Our approach is adaptable to any complex DNA library, and fundamentally changes how these libraries can be parsed, maintained, propagated, and characterized.     

Genome-wide requirements for resistance to functionally distinct DNA-damaging agents

The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed the effects of 12 closely related DNA-damaging agents on the complete pool of ~4,700 barcoded homozygous deletion strains of Saccharomyces cerevisiae. In our protocol, deletion strains are pooled together and grown competitively in the presence of compound. Relative strain sensitivity is determined by hybridization of PCR-amplified barcodes to an oligonucleotide array carrying the barcode complements. These screens identified genes in well-characterized DNA-damage-response pathways as well as genes whose role in the DNA-damage response had not been previously established. High-throughput individual growth analysis was used to independently confirm microarray results. Each compound produced a unique genome-wide profile. Analysis of these data allowed us to determine the relative importance of DNA-repair modules for resistance to each of the 12 profiled compounds. Clustering the data for 12 distinct compounds uncovered both known and novel functional interactions that comprise the DNA-damage response and allowed us to define the genetic determinants required for repair of interstrand cross-links. Further genetic analysis allowed determination of epistasis for one of these functional groups.     

Correlated rates of synonymous site evolution across plant genomes

Synonymous substitution rates have been shown to vary among evolutionary lineages of both nuclear and organellar genes across a broad range of taxonomic groups. In animals, rate heterogeneity does not appear to be correlated across nuclear and mitochondrial genes. In this paper, we contrast substitution rates in two plant groups and show that grasses evolve more rapidly than palms at synonymous sites in a mitochondrial, a nuclear, and a plastid gene. Furthermore, we show that the relative rates of synonymous substitution between grasses and palms are similar at the three loci. The correlation in synonymous substitution rates across genes is particularly striking because the three genes evolve at very different absolute rates. In contrast, relative rates of nonsynonymous substitution are not conserved among the three genes.