A novel environmental DNA approach to quantify the cryptic invasion of non‐native genotypes

The invasion of non‐native species that are closely related to native species can lead to competitive elimination of the native species and/or genomic extinction through hybridization. Such invasions often become serious before they are detected, posing unprecedented threats to biodiversity. A Japanese native strain of common carp (Cyprinus carpio) has become endangered owing to the invasion of non‐native strains introduced from the Eurasian continent. Here, we propose a rapid environmental DNA‐based approach to quantitatively monitor the invasion of non‐native genotypes. Using this system, we developed a method to quantify the relative proportion of native and non‐native DNA based on a single‐nucleotide polymorphism using cycling probe technology in real‐time PCR. The efficiency of this method was confirmed in aquarium experiments, where the quantified proportion of native and non‐native DNA in the water was well correlated to the biomass ratio of native and non‐native genotypes. This method provided quantitative estimates for the proportion of native and non‐native DNA in natural rivers and reservoirs, which allowed us to estimate the degree of invasion of non‐native genotypes without catching and analysing individual fish. Our approach would dramatically facilitate the process of quantitatively monitoring the invasion of non‐native conspecifics in aquatic ecosystems, thus revealing a promising method for risk assessment and management in biodiversity conservation.     

A rapid simple approach to quantify chromosome conformation capture

Chromosome conformation capture (3C) is a powerful tool to study DNA looping. The procedure generates chimeric DNA templates after ligation of restriction enzyme fragments juxtaposed in vivo by looping. These unique ligation products (ULPs) are typically quantified by gel-based methods, which are practically inefficient. Taqman probes may be used, but are expensive. Cycle threshold (Ct) determined using SYBR Green, an inexpensive alternative, is hampered by non-specific products and/or background fluorescence, both due to high template/ULP ratio. SYBR Green melting curve analysis (MCA) is a well-known qualitative tool for assessing PCR specificity. Here we present for the first time MCA as a quantitative tool (qMCA) to compare template concentrations across different samples and apply it to 3C to assess looping among remote elements identified by STAT1 and IRF1 ChIP-chip at the interferon-γ responsive CIITA and SOCS1 loci. This rapid, inexpensive approach provided highly reproducible identification and quantification of ULPs over a significant linear range. Therefore, qMCA is a robust method to assess chromatin looping in vivo, and overcomes several drawbacks associated with other approaches. Our data suggest that basal and induced looping is a involving remote enhancers is a common mechanism at IFNγ-regulated targets.     

Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy

Ecosystems have a limited buffering capacity of multiple ecosystem functions against biodiversity loss (i.e. low multifunctional redundancy). We developed a novel theoretical approach to evaluate multifunctional redundancy in a microbial community using the microbial genome database (MBGD) for comparative analysis. In order to fully implement functional information, we defined orthologue richness in a community, each of which is a functionally conservative evolutionary unit in genomes, as an index of community multifunctionality (MF). We constructed a graph of expected orthologue richness in a community (MF) as a function of species richness (SR), fit the power function to SR (i.e. MF = cSR^a), and interpreted the higher exponent a as the lower multifunctional redundancy. Through a microcosm experiment, we confirmed that MF defined by orthologue richness could predict the actual multiple functions. We simulated random and non-random community assemblages using full genomic data of 478 prokaryotic species in the MBGD, and determined that the exponent in microbial communities ranged from 0.55 to 0.75. This exponent range provided a quantitative estimate that a 6.6–8.9% loss limit in SR occurred in a microbial community for an MF reduction no greater than 5%, suggesting a non-negligible initial loss effect of microbial diversity on MF.     

Novel approach to quantify immobilized-enzyme distributions

The quantitative intraparticle enzyme distribution of Assemblase, an industrially employed polydisperse immobilized penicillin-G acylase, was measured. Because of strong autofluorescence of the carrier, the generally applied technique of confocal scanning microscopy could not be used; light microscopy was our method of choice. To do so, Assemblase particles of various sizes were sectioned, labeled with antibodies specifically against the enzyme, and analyzed light microscopically. Image analysis software was developed and used to determine the intraparticle enzyme distribution, which was found to be heterogeneous, with most enzyme located in the outer regions of the particles. Larger particles showed steeper gradients than smaller ones. A mathematical representation of the intraparticle profiles, based on in-stationary enzyme diffusion into the particles, was validated successfully for a broad range of particle sizes using data for volume-averaged particle size and enzyme loading. The enzyme gradients determined in this work will be used as input for a physical model that quantitatively describes the complex behavior of Assemblase. Such a physical model will lead to identification of the current bottlenecks in Assemblase and can serve as a starting point for the design of improved biocatalysts that also may be based on intelligent use of enzyme gradients.     

A novel system to quantify intestinal lipid digestion and transport

The zebrafish larva is a powerful tool for the study of dietary triglyceride (TG) digestion and how fatty acids (FA) derived from dietary lipids are absorbed, metabolized and distributed to the body. While fluorescent FA analogues have enabled visualization of FA metabolism, methods for specifically assaying TG digestion are badly needed. Here we present a novel High Performance Liquid Chromatography (HPLC) method that quantitatively differentiates TG and phospholipid (PL) molecules with one or two fluorescent FA analogues. We show how this tool may be used to discriminate between undigested and digested TG or phosphatidylcholine (PC), and also the products of TG or PC that have been digested, absorbed and re-synthesized into new lipid molecules. Using this approach, we explored the dietary requirement of zebrafish larvae for phospholipids. Here we demonstrate that dietary TG is digested and absorbed in the intestinal epithelium, but without dietary PC, TG accumulates and is not transported out of the enterocytes. Consequently, intestinal ER stress increases and the ingested lipid is not available support the energy and metabolic needs of other tissues. In TG diets with PC, TG is readily transported from the intestine and subsequently metabolized.     

A new approach to quantify trabecular resorption adjacent to cemented knee arthroplasty

A new micro-computed tomography (μCT) image processing approach to estimate the loss of cement-bone interlock was developed using the concept that PMMA cement flows and cures around trabeculae during the total knee arthroplasty procedure. The initial mold shape of PMMA cement was used to estimate the amount of interdigitated bone at the time of implantation and following in vivo service using enbloc human postmortem retrievals. Laboratory prepared specimens, where there would be no biological bone resorption, were used as controls to validate the approach and estimate errors. The image processing technique consisted of identifying bone and cement from the μCT scan set, dilation of the cement to identify the cement cavity space, and Boolean operations to identify the different components of the interdigitated cement-bone regions. For laboratory prepared specimens, there were small errors in the estimated resorbed bone volume fraction (reBVfr=0.11 ± 0.09) and loss in contact area fraction (CAfr=0.06 ± 0.15). These values would be zero if there were no error in the method. For the postmortem specimens, the resorbed volume fraction (reBVfr=0.85 ± 0.16) was large, meaning that only 15% of the cement mold shape was still filled with bone. The loss of contact area fraction (CAfr=0.84 ± 0.17) was similarly large. This new approach provides a convenient method to visualize and quantify trabecular bone loss from interdigitated regions from postmortem retrievals. The technique also illustrates for the first time that there are dramatic changes in how bone is fixed to cement following in vivo service.     

Computerized approach using autoradiography to quantify atrial natriuretic peptide receptors in the DOCA-salt hypertensive rat kidney.

The alteration of atrial natriuretic peptide (ANP) receptors was investigated in the kidney of deoxycorticosterone acetate (DOCA)-salt treated hypertensive rats. The absolute amount of renal ANP receptors was determined in a membrane homogenate binding study of rat whole kidneys. Administration of DOCA-salt led to a decrease in renal ANP receptors after 3 weeks (prehypertensive state) and 6 weeks (established hypertensive state) of treatment. In vitro macro-autoradiography (ARG) was then performed with [125I]ANP to localize and to quantitate specific renal ANP receptors. ARG revealed that specific ANP binding was distributed mainly over the renal cortex with the inner medulla next in frequency. Renal ANP receptors were therefore quantified over the cortex and the inner medulla using the computerized microdensitometry of ARG. A significant reduction in renal ANP receptors was observed in the DOCA-salt treated rats after 3 and 6 weeks of treatment with decrements observed in both the cortex and inner medulla. These alterations may be related to the pathophysiology of hypertension.     

A novel colorimetric method to quantify tannase activity of viable bacteria

A novel colorimetric method to quantify tannase activity of viable tannase-producing bacterial strains was developed through application of a visual reading method that was to detect the activity qualitatively. The novel method was sensitive enough to quantify the marginal tannase activity of strains that could not be otherwise measured by conventional spectrophotometric or colorimetric methods.     

A model-driven approach to quantify migration patterns: individual, regional and yearly differences

1.?Animal migration has long intrigued scientists and wildlife managers alike, yet migratory species face increasing challenges because of habitat fragmentation, climate change and over-exploitation. Central to the understanding migratory species is the objective discrimination between migratory and nonmigratory individuals in a given population, quantifying the timing, duration and distance of migration and the ability to predict migratory movements. 2.?Here, we propose a uniform statistical framework to (i) separate migration from other movement behaviours, (ii) quantify migration parameters without the need for arbitrary cut-off criteria and (iii) test predictability across individuals, time and space. 3.?We first validated our novel approach by simulating data based on established theoretical movement patterns. We then formulated the expected shapes of squared displacement patterns as nonlinear models for a suite of movement behaviours to test the ability of our method to distinguish between migratory movement and other movement types. 4.?We then tested our approached empirically using 108 wild Global Positioning System (GPS)-collared moose Alces alces in Scandinavia as a study system because they exhibit a wide range of movement behaviours, including resident, migrating and dispersing individuals, within the same population. Applying our approach showed that 87% and 67% of our Swedish and Norwegian subpopulations, respectively, can be classified as migratory. 5.?Using nonlinear mixed effects models for all migratory individuals we showed that the distance, timing and duration of migration differed between the sexes and between years, with additional individual differences accounting for a large part of the variation in the distance of migration but not in the timing or duration. Overall, the model explained most of the variation (92%) and also had high predictive power for the same individuals over time (69%) as well as between study populations (74%). 6.?The high predictive ability of the approach suggests that it can help increase our understanding of the drivers of migration and could provide key quantitative information for understanding and managing a broad range of migratory species.     

Selective AV nodal vagal stimulation improves hemodynamics during acute atrial fibrillation in dogs

Although the atrioventricular node (AVN) plays a vital role in blocking many of the atrial impulses from reaching the ventricles during atrial fibrillation (AF), a rapid irregular ventricular rate nevertheless persists. The goals of the present study were to explore the feasibility of novel epicardial selective vagal nerve stimulation for slowing of the ventricular rate during AF and to characterize the hemodynamic benefits in vivo. Electrophysiological-echocardiographic experiments were performed on 11 anesthetized open-chest dogs. Hemodynamic measurements were performed during three distinct periods: 1) sinus rate, 2) AF, and 3) AF with vagal nerve stimulation. AF was associated with significant deterioration of all measured parameters (P < 0.025). The vagal nerve stimulation produced slowing of the ventricular rate, significant reversal of the pressure and contractile indexes (P < 0.025), and a sharp reduction in one-half of the abortive ventricular contractions. The present study provides comprehensive evidence that slowing of the ventricular rate during AF by selective ganglionic stimulation of the vagal nerves that innervate the AVN successfully improved the hemodynamic responses.     

A novel method to quantify H-ATPase-dependent Na transport across plasma membrane vesicles

To prevent sodium toxicity in plants, Na⁺ is excluded from the cytosol to the apoplast or the vacuole by Na⁺/H⁺ antiporters. The secondary active transport of Na⁺ to apoplast against its electrochemical gradient is driven by plasma membrane H⁺-ATPases that hydrolyze ATP and pump H⁺ across the plasma membrane. Current methods to determine Na⁺ flux rely either on the use of Na-isotopes (²²Na) which require special working permission or sophisticated equipment or on indirect methods estimating changes in the H⁺ gradient due to H⁺-ATPase in the presence or absence of Na⁺ by pH-sensitive probes. To date, there are no methods that can directly quantify H⁺-ATPase-dependent Na⁺ transport in plasma membrane vesicles. We developed a method to measure bidirectional H⁺-ATPase-dependent Na⁺ transport in isolated membrane vesicle systems using atomic absorption spectrometry (AAS). The experiments were performed using plasma membrane-enriched vesicles isolated by aqueous two-phase partitioning from leaves of Populus tomentosa. Since most of the plasma membrane vesicles have a sealed right-side-out orientation after repeated aqueous two-phase partitioning, the ATP-binding sites of H⁺-ATPases are exposed towards inner side. Leaky vesicles were preloaded with Na⁺ sealed for the study of H⁺-ATPase-dependent Na⁺ transport. Our data implicate that Na⁺ movement across vesicle membranes is highly dependent on H⁺-ATPase activity requiring ATP and Mg²⁺ and displays optimum rates of 2.50 μM Na⁺ mg^− 1 membrane protein min^− 1 at pH 6.5 and 25 °C. In this study, for the first time, we establish new protocols for the preparation of sealed preloaded right-side-out vesicles for the study of H⁺-ATPase-dependent Na⁺ transport. The results demonstrate that the Na⁺ content of various types of plasma membrane vesicle can be directly quantified by AAS, and the results measured using AAS method were consistent with those determined by the previous established fluorescence probe method. The method is a convenient system for the study of bidirectional H⁺-ATPase-dependent Na⁺ transport with membrane vesicles.     

A novel approach to quantify and locate potential microrefugia using topoclimate,climate stability,and isolation from the matrix

Ecologists are increasingly recognizing the conservation significance of microrefugia, but it is inherently difficult to locate these small patches with unusual climates, and hence they are also referred to as cryptic refugia. Here we introduce a new methodology to quantify and locate potential microrefugia using fine‐scale topoclimatic grids that capture extreme conditions, stable climates, and distinct differences from the surrounding matrix. We collected hourly temperature data from 150 sites in a large (200 km by 300 km) and diverse region of New South Wales, Australia, for a total of 671 days over 2 years. Sites spanned a range of habitats including coastal dune shrublands, eucalypt forests, exposed woodland ridges, sheltered rainforest gullies, upland swamps, and lowland pastures. Climate grids were interpolated using a regional regression approach based on elevation, distance to coast, canopy cover, latitude, cold‐air drainage, and topographical exposure to winds and radiation. We identified extreme temperatures on two separate climatic gradients: the 5th percentile of minimum temperatures and the 95th percentile of maximum temperatures. For each gradient, climatic stability was assessed on three different time scales (intra‐seasonal, intra‐annual and inter‐annual). Differences from the matrix were assessed using a moving window with a 5 km radius. We averaged the Z‐scores for these extreme, stable and isolated climates to identify potential locations of microrefugia. We found that our method successfully predicted the location of communities that were considered to occupy refugia, such as rainforests that have progressively contracted in distribution over the last 2.5 million years, and alpine grasslands that have contracted over the last 15 thousand years. However, the method was inherently sensitive to the gradient selected and other aspects of the modelling process. These uncertainties could be dealt with in a conservation planning context by repeating the methodology with various parameterizations and identifying areas that were consistently identified as microrefugia.     

A novel approach to improve the efficacy of tumour ablation during cryosurgery

Freezing tumours and ablating it using cryosurgery is becoming a popular surgical procedure for treatment of carcinomas. In order to improve the efficiency of the cryosurgical procedure different approaches have been implemented till now, e.g., injecting high thermal conductivity fluid inside the tumour, low latent heat fluids inside the tumour prior to cryosurgery etc. These techniques improve the cryosurgical process to some extent but lack in minimising the damage to the surrounding healthy tissues. In this study, a novel concept is proposed which advocates the use of solutions with specific thermophysical properties around the interface of tumour. Numerical modelling has been done to determine the location of the ice fronts in the presence of this solution around the boundary of the tumour. It is noticed that in the presence of solution layer, owing to its distinct thermophysical properties like low thermal conductivity, not only the cellular destruction is enhanced but also the damage to the surrounding healthy tissue is minimised. Further, results indicate that this strategy leads to a faster ablation rate reducing the surgical time immensely. Also, an optimal offset, the minimum distance between the tip of cryoprobe and the boundary of the tumour, is identified for a given tumour radius with a given active length which gives maximum tumour necrosis in less time. This optimal offset which has been identified for each case will help the surgeons in proper planning of cryosurgery and improving the effectiveness of this technique greatly, making it a better treatment modality than its counterparts in many ways. It is also observed that for a 2 mm increase in activelength of the cryoprobe, the decrease in optimal offset is approximately 1 mm, i.e. optimal offset decreases linearly with an increase in the activelength for a given radius of the tumour. Also, for tumour with different radii, ranging between 10 mm to 15 mm, with same active length, the time taken for complete ablation by the larger tumour is nearly 2.7 times the time taken by the smaller one for every 2.5 mm increase in the tumour radius.     

Pericardial delivery of omega-3 fatty acid: a novel approach to reducing myocardial infarct sizes and arrhythmias

O2-carrying fluids based on hemoglobin (Hb) are in various stages of clinical trials to determine their suitability as O2-carrying plasma expanders. Polymerized Hb solutions are characterized by their vasoactivity, low O2 affinity, oncotic effect, prolonged shelf life, and stability. Physiological responses to facilitated O2 transport after exchange transfusion with polymerized bovine Hb (PBH) were studied in the hamster window chamber model during acute moderate anemia to determine how PBH affects microvascular perfusion and tissue oxygenation. The anemic state [29% hematocrit (Hct)] was induced by hemodilution with a plasma expander (70 kDa dextran). After hemodilution, animals were randomly assigned to different exchange transfusion groups. Study groups were based on the concentration of PBH used, namely: PBH at 13 g Hb/dl [PBH13], PBH diluted to 8 (PBH8) or 4 (PBH4) g Hb/dl in albumin solution at matching colloidal osmotic pressure (COP), and no PBH (only albumin solution) at matching COP (PBH0). Measurement of systemic parameters, microvascular hemodynamics, capillary perfusion, and intravascular and tissue O2 levels was performed at 18% Hct. Restitution of O2-carrying capacity with PBH13 increased arterial pressure and triggered vasoconstriction, low perfusion, and high peripheral resistance. PBH4 and PBH0 exhibited lower arterial pressures compared with PBH13. Exchange transfused animals with PBH8 and PBH4 better maintained perfusion and functional capillary density than PBH13. Blood gas parameters and acid-base balance were recovered proportional to microvascular perfusion. Arterial O2 tensions were improved with PBH4 and PBH8 by preventing O2 precapillary release and increasing O2 reserve. Further studies to establish PBH optimal dosage, efficacy, safety, and its effect on outcome are indicated before Hb-based O2-carrying blood substitutes are implemented in routine practice.     

A novel approach to prezizaane sesquiterpenes

Prezizaane sesquiterpenes are an olfactorily interesting class of tricyclic natural products, which occur in some precious perfumery raw materials. These compounds are biosynthetically derived from farnesyl pyrophosphate via cyclization, but some questions regarding the stereoselectivity of this process have not yet been answered. We discuss a novel and concise access to the tricyclic framework of these sesquiterpenes, as exemplified by the synthesis of (+/-)-5-epi-sesquithuriferone (5-epi-4).     

A light-reflectance meter to quantify silvering during smolting in Atlantic salmon

An easy-to-construct apparatus is described to quantify changes in silvering during smolting. A modulated visible-red light emitter/receiver unit converts light reflected from the flank of the fish into a DC voltage, the voltage being proportional to the intensity of the reflected light.